IDEA puts all pom.xml files into ignoredFiles on git checkout

Hi,
A really annoying thing keeps happening whenver I change branch with a git checkout - IDEA puts all my Maven module pom.xml files into a <option name="ignoredFiles"> element in .idea/misc.xml, so all modules disappear from the project. I have to manually remove this section from misc.xml. Normally I do the git checkout on command line as there are a few  glitches in IDEA's git integration. I think it also happens if I git  checkout within IDEA - I can verify this if this is not a known issue  and you need me to. Is there a workaround, and should I raise this as a bug?
Alex