I haven't been able to reproduce this on demand so unfortunately I don't have a proper test case for this but I have twice found that removing my module and readding it somehow caused one of the juce modules to dissapear. I was able to re-add the module and continue on but somethings up with that. I also tried removing juce_core module (don't ask why) and it caused the introjucer to crash. Apologies for not having a stack trace or proper test case but felt it's worth mentioning that something's up when it comes to removing and/or adding modules (I think more to do with removing). I'll see if I can catch them again but I've finished up most of my module work now so not sure how likely I'll hit it again.
this is latest introjucer of course, and I'm on osx 10.8 running the introjucer with it's default debug build config.