IB doesn't sync with Xcode on a new project (related to project path)

Hey everybody!
I've got very strange behavior of the Interface Builder.
I've got ~/Documents/Projects folder. I start Xcode and choose to create a new iPhone project. I don't change anything, just open the main controller's XIB file with IB and I can see the gray sync status in the Document window there. So, IB is out of sync. But, if I create a project in some other location it works fine! Even if I recreate the Projects folder at the same location it works fine! And it all works for only a few days. Then, this bug occurs again.
This bug disappoints me a lot and I'd appreciate any help. Thanks in advance!
PS. The bug was discovered on Mac OS X 10.6.4 with Xcode 3.2.4, but has been verified also on 10.6.4/3.2.5 and 10.6.5/3.2.4.

Of course, I reinstalled SDK, cleared caches, preferences and so on.
Tech Guru, thank you for your replies, but it seems I posted my question in the wrong place. On the whole forum the only person payed attention to my issue is you Maybe you can advice me the right place?

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