Reposting my still unresolved (and very annoying) bug from the BerliOS tracker: http://alpha0010.github.io/cb-history/bugs/19263.html
When saving a project after modification (addition of project files, libraries, etc), all the slashes in the project .cbp file flip to those appropriate for the current platform. However, this affects even those targets intended for other platforms or to which no modification has taken place.
As a result, when modifying the same project from both windows and linux, every alternate save switches all / slashes to \ and vice versa, which makes an unnecessary mess in the revision control system.
Ideally when saving, CB should standardise on posix style forward slashes, and when running on windows treat those as backslashes but still save as posix style to avoid unnecessary flip-flopping on file save.
An example of the changes in the .cbp caused by modifying and saving a project under windows although the affected target is a linux target:
What version are you using?
This should no longer be problem with 13.12 (if I'm not mistaken) and latest night builds for sure!
This is very recent - the latest nightly, SVN 9855.

This is bad... I thought is has been fix, but it is not. See this discussion http://forums.codeblocks.org/index.php/topic,16596.15.html
I just tested it on windows 7 with a pre 13.12 revision and with actual trunk on linux.
It seems only link libraries that contain a path are affected.
Can you confirm this ?
Normal files seem to be okay.
The discussed change is from September 2012: https://sourceforge.net/p/codeblocks/code/8393
Should be fixed in trunk (svn r9859).
If not, please reopen the ticket.