I have updated my Ubuntu box to 11.10 and then Eclipse also have been updated to 3.7.0 Indigo with CDT 8.0.1
Then the following problem occurs:
Ok here is what worked for me:
deleted the path to the header files I created from the include path
compiled the project (obviously the compiler complains since it is missing user-defined headers)
reinserted the path to the header files I created
compiled the project again - worked perfectly
I can't explain the case :(