java.io.FileNotFoundException: <path_to_project_dir>/.idea/libraries/.svn (Is a directory)

We've recently upgraded to TeamCity 6.0 and found this problem.
We are using 'Agent-side checkout' option with Subversion as VCS (we can't use Server-side checkout at the moment). Our project is in .IPR now, so we tried to convert it to idea-project. But during build the following error appears:

[Step 2/3] Using runner: JPS
............................
[13:30:28]: [Step 2/3] java.io.FileNotFoundException: /var/tainted/build-agent/work/Server_unit_tests/server/.idea/libraries/.svn (Is a directory)

It seems TeamCity is trying to add .svn as a library. Can this be fixed?