@Loaden:
Did you remove the devel and output folder before building or did you make rebuild (clean and build) ?
If that's not enough remove the pch's manually.
You should also remove all occurrences of scintilla in the link library list, where a target is linked against libcodeblocks, to avoid double linking and possible crashes (we had this in wxSmith with libtxml).
I attach a patch for C::B core that works on linux.