Cannot get Versioned Settings to work

Hi,

We are trying to move all our TeamCity configuration into GitHub but have so fair only encountered errors coming from jgit

Steps to reproduce:
- create a new empty repository on github (with README file)
- TeamCity -> Administration -> Root Project -> VCS Roots -> New VCS root with new repo -> Test Connection -> Success
- TeamCity -> Administration -> Root Project -> Versioned Settings ->
-- Enable Sync
-- Configure VCS root created above
-- Use "always use current settings"
-- Settings format: xml
-- Apply -> Error
-- Try clicking "Commit current project settings..." -> Error

I've tried:
- both VCS connection methods (https/ssh).
- deleting everything and starting over.
- clearing the TeamCity vcs caches in the Diagnostics view.
- upgrading TeamCity to the latest version

I don't know what else to try and use this feature and hope someone can tell me where I am going wrong.

Cheers
Oliver

== Error when trying to use github ssh url ==
[2018-05-31 19:11:52,435] WARN [sister - Save 1] - ggers.vcs.git.GitCommitSupport - Error while pushing a commit, root "teamcity-configuration2" {instance id=803, parent internal id=30, parent id=TeamcityConfiguration2, description: "git@github.com:FakeOrganization/teamcity-configuration.git#refs/heads/master"}, revision AnyObjectId[f11382af4f269a54bc84654ff6b80ad1f6d3654c], destination refs/heads/master
org.eclipse.jgit.errors.TransportException: git@github.com:FakeOrganization/teamcity-configuration.git: Short read of block.
at org.eclipse.jgit.transport.BasePackPushConnection.doPush(BasePackPushConnection.java:225)
at org.eclipse.jgit.transport.BasePackPushConnection.push(BasePackPushConnection.java:160)
at org.eclipse.jgit.transport.PushProcess.execute(PushProcess.java:165)
at org.eclipse.jgit.transport.Transport.push(Transport.java:1200)
at org.eclipse.jgit.transport.Transport.push(Transport.java:1246)
at jetbrains.buildServer.buildTriggers.vcs.git.GitCommitSupport$GitCommitPatchBuilder.commit(GitCommitSupport.java:171)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DirectoryBasedTransactionCommitter.doCommit(DirectoryBasedTransactionCommitter.java:162)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DirectoryBasedTransactionCommitter.commit(DirectoryBasedTransactionCommitter.java:169)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DelayedCommitPerSettingsRootStrategy.commit(DelayedCommitPerSettingsRootStrategy.java:55)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DelayedCommitPerSettingsRootStrategy.run(DelayedCommitPerSettingsRootStrategy.java:223)
at jetbrains.buildServer.serverSide.impl.versionedSettings.ConfigChangesCommitterImpl.onPersist(ConfigChangesCommitterImpl.java:90)
at jetbrains.buildServer.serverSide.impl.versionedSettings.ConfigChangesCommitterImpl.onPersist(ConfigChangesCommitterImpl.java:36)
at jetbrains.buildServer.serverSide.impl.projects.ConfigurationPersister.notifyConfigChangesListener(ConfigurationPersister.java:125)
at jetbrains.buildServer.serverSide.impl.projects.ConfigurationPersister.saveEntity(ConfigurationPersister.java:57)
at jetbrains.buildServer.serverSide.impl.projects.ConfigurationPersister.saveProjectAndInnerEntities(ConfigurationPersister.java:60)
at jetbrains.buildServer.serverSide.impl.projects.ProjectImpl.doPersistInternally(ProjectImpl.java:727)
at jetbrains.buildServer.serverSide.impl.projects.ProjectImpl.access$700(ProjectImpl.java:548)
at jetbrains.buildServer.serverSide.impl.projects.ProjectImpl$13$1.run(ProjectImpl.java:5)
at jetbrains.buildServer.serverSide.impl.projects.PersistTaskImpl.run(PersistTaskImpl.java:34)
at jetbrains.buildServer.serverSide.impl.projects.BackgroundPersisterImpl$RunTask.lambda$run$0(BackgroundPersisterImpl.java:4)
at jetbrains.buildServer.util.NamedThreadFactory.executeWithNewThreadName(NamedThreadFactory.java:71)
at jetbrains.buildServer.serverSide.impl.projects.BackgroundPersisterImpl$RunTask.run(BackgroundPersisterImpl.java:13)
at jetbrains.buildServer.configuration.FilesWatcher.runActionWithDisabledObserver(FilesWatcher.java:229)
at jetbrains.buildServer.serverSide.impl.projects.BackgroundPersisterImpl$FlushOnDisk.run(BackgroundPersisterImpl.java:44)
at jetbrains.buildServer.util.NamedThreadFactory.executeWithNewThreadName(NamedThreadFactory.java:71)
at jetbrains.buildServer.util.ExceptionUtil$1.run(ExceptionUtil.java:41)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.EOFException: Short read of block.
at org.eclipse.jgit.util.IO.readFully(IO.java:248)
at org.eclipse.jgit.transport.PacketLineIn.readLength(PacketLineIn.java:186)
at org.eclipse.jgit.transport.SideBandInputStream.needDataPacket(SideBandInputStream.java:158)
at org.eclipse.jgit.transport.SideBandInputStream.read(SideBandInputStream.java:140)
at org.eclipse.jgit.util.IO.readFully(IO.java:246)
at org.eclipse.jgit.transport.PacketLineIn.readLength(PacketLineIn.java:186)
at org.eclipse.jgit.transport.PacketLineIn.readString(PacketLineIn.java:138)
at org.eclipse.jgit.transport.BasePackPushConnection.readStringLongTimeout(BasePackPushConnection.java:381)
at org.eclipse.jgit.transport.BasePackPushConnection.readStatusReport(BasePackPushConnection.java:322)
at org.eclipse.jgit.transport.BasePackPushConnection.doPush(BasePackPushConnection.java:208)
... 32 more

== Error when trying to use github https url ==
[2018-05-31 18:56:48,415] WARN [uled executor 3] - ggers.vcs.git.GitCommitSupport - Error while pushing a commit, root "teamcity-configuration2" {instance id=799, parent internal id=30, parent id=TeamcityConfiguration2, description: "https://github.com/FakeOrganization/teamcity-configuration#refs/heads/master"}, revision AnyObjectId[86014824700bf9b3282885c136e5b884f27eceeb], destination refs/heads/master
org.eclipse.jgit.errors.TransportException: https://github.com/FakeOrganization/teamcity-configuration: Starting read stage without written request data pending is not supported
at org.eclipse.jgit.transport.TransportHttp$MultiRequestService.execute(TransportHttp.java:979)
at org.eclipse.jgit.transport.TransportHttp$Service$HttpExecuteStream.read(TransportHttp.java:913)
at org.eclipse.jgit.util.io.UnionInputStream.read(UnionInputStream.java:145)
at java.io.FilterInputStream.read(FilterInputStream.java:133)
at org.eclipse.jgit.util.io.TimeoutInputStream.read(TimeoutInputStream.java:112)
at org.eclipse.jgit.util.IO.readFully(IO.java:246)
at org.eclipse.jgit.transport.PacketLineIn.readLength(PacketLineIn.java:186)
at org.eclipse.jgit.transport.SideBandInputStream.needDataPacket(SideBandInputStream.java:158)
at org.eclipse.jgit.transport.SideBandInputStream.read(SideBandInputStream.java:140)
at org.eclipse.jgit.util.IO.readFully(IO.java:246)
at org.eclipse.jgit.transport.PacketLineIn.readLength(PacketLineIn.java:186)
at org.eclipse.jgit.transport.PacketLineIn.readString(PacketLineIn.java:138)
at org.eclipse.jgit.transport.BasePackPushConnection.readStringLongTimeout(BasePackPushConnection.java:381)
at org.eclipse.jgit.transport.BasePackPushConnection.readStatusReport(BasePackPushConnection.java:322)
at org.eclipse.jgit.transport.BasePackPushConnection.doPush(BasePackPushConnection.java:208)
at org.eclipse.jgit.transport.TransportHttp$SmartHttpPushConnection.doPush(TransportHttp.java:817)
at org.eclipse.jgit.transport.BasePackPushConnection.push(BasePackPushConnection.java:160)
at org.eclipse.jgit.transport.PushProcess.execute(PushProcess.java:165)
at org.eclipse.jgit.transport.Transport.push(Transport.java:1200)
at org.eclipse.jgit.transport.Transport.push(Transport.java:1246)
at jetbrains.buildServer.buildTriggers.vcs.git.GitCommitSupport$GitCommitPatchBuilder.commit(GitCommitSupport.java:171)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DirectoryBasedTransactionCommitter.doCommit(DirectoryBasedTransactionCommitter.java:162)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DirectoryBasedTransactionCommitter.commit(DirectoryBasedTransactionCommitter.java:169)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DelayedCommitPerSettingsRootStrategy.commit(DelayedCommitPerSettingsRootStrategy.java:55)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DelayedCommitPerSettingsRootStrategy.access$200(DelayedCommitPerSettingsRootStrategy.java:67)
at jetbrains.buildServer.serverSide.impl.versionedSettings.DelayedCommitPerSettingsRootStrategy$Commit.run(DelayedCommitPerSettingsRootStrategy.java:6)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at jetbrains.buildServer.util.executors.TeamCityScheduledThreadPoolExecutor$RunnableScheduledFutureWrapper.run(TeamCityScheduledThreadPoolExecutor.java:77)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Version:
2017.2.4 (build 51228)

Java Settings
Java version: 1.8.0_161
Java VM info: Java HotSpot(TM) Server VM (32 bit)
Java Home path: C:\dev\TeamCity\TeamCity2017.2\jre
Server: Apache Tomcat/8.5.23
JVM arguments:
-Djava.util.logging.config.file=C:\dev\TeamCity\TeamCity2017.2\bin\..\conf\logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -Xrs -Xmx1g -Dteamcity.configuration.path=../conf/teamcity-startup.properties -Dlog4j.configuration=file:../conf/teamcity-server-log4j.xml -Dteamcity_logs=C:\dev\TeamCity\TeamCity2017.2\bin\..\logs -Dcatalina.base=C:\dev\TeamCity\TeamCity2017.2\bin\.. -Dcatalina.home=C:\dev\TeamCity\TeamCity2017.2\bin\.. -Djava.io.tmpdir=C:\dev\TeamCity\TeamCity2017.2\bin\..\temp