I have seen wierd things with the latest versions (1.0.1 and later) and "special libraries"
It happened again after I described it in this post BUG in Arduino IDE 1.0.1 and 1.0.2 when you have a library with name Arduino - Suggestions for the Arduino Project - Arduino Forum
Renaming the folder only helps for the run you are doing. Next time you start the Arduino IDE it piced it up again. So the problem is not name related.
Not sure it is related to the problem of the PO but it does sound a bit like it.
Anyway posting the full sketch should be the starting point.
Best regards
Jantje