Turns out it has something to do with my .codeblocks folder (During investigation I tried to move it and that fixed the issue). Although it makes the EOF LF by default now. (But the project and all the files were created with existing profile and EOF CR+LF + consistent EOFs). Any help where to look in the profile for this issue? Or should I send over my profile in tar.gz?
I also tried cleaning up /usr/local/(lib, share, inlcude), but the appropriate folders were just empty folders.