Teamcity slow. 100% disk usage

Our entire build process is too slow in teamcity on a particular server (20 minutes) but fast when running via commandline (5 minutes)

When just running a small nant script, teamcity takes a minute and a half, but the same script from commandline takes milliseconds.

Here is the performance while the build runs. 100% disk usage all the way through:

Teamcity runs the following command:

C:\Nant\bin\NAnt.exe -buildfile:C:\TeamCityNew\buildAgent\work\95a3865a544f7c85\build\Desmat.build -extension:C:\TeamCityNew\buildAgent\plugins\dotnetPlugin\bin\JetBrains.BuildServer.NAntLoggers.dll -listener:JetBrains.BuildServer.NAntLoggers.NAntListener

Here is the output from teamcity:

[11:34:42]Step 1/1: Take Web App Offline (NAnt) (1m:22s)
[11:34:42][Step 1/1] Starting: C:\Nant\bin\NAnt.exe -buildfile:C:\Build\Desmat.build -extension:C:\TeamCityNew\buildAgent\plugins\dotnetPlugin\bin\JetBrains.BuildServer.NAntLoggers.dll -listener:JetBrains.BuildServer.NAntLoggers.NAntListener
[11:34:42][Step 1/1] in directory: C:\TeamCityNew\buildAgent\work\95a3865a544f7c85
[11:36:04][Step 1/1] Buildfile: file:///C:/Build/Desmat.build
[11:36:04][Step 1/1] Target framework: Microsoft .NET Framework 4.0
[11:36:04][Step 1/1]
[11:36:04][Step 1/1] Process exited with code 0

Here is the content of the build file:

<project name="Desmat" basedir=".">
<target name="takeAppOffline" description="Takes the web application offline by placing the app_offline.htm file in the web root directory" depends="config">
<copy file="..\build\app_offline.htm.online" overwrite="true" tofile="${webPath}\app_offline.htm" failonerror="false"/>
</target>

</project>

Please can you assist me in how to correct this disk usage? Please let me know what files you may need. I have tried in various versions of teamcity with the same result, including the latest version.