We had a problem building our project using the IPR runner today. We'd added some JAXB objects which are generated and compiled as part of our ant build, so we registered the task to be executed before compilation. The source code was generated in a src-generated directory at the same level as src, and this directory was registered as a source folder in the project settings. This all worked fine in local, but running it within TeamCity didn't work - the compilation failed because it couldn't find the generated classes. What seems to happen is the build process starts, notices that the src-generated directory doesn't exist and de-registers it as a source folder, then after that runs the task that creates the folder. The workaround is to have the src-generated dir checked into subversion, and have clean simply clean its contents, not remove the whole folder.
Shall I file a JIRA?