Okay, I've done some further testing specifically on my saved sublime-projects. It would seem if I create the project from scratch (same destination directory, no symlinks involved in either case) it starts working correctly. Loading from the .sublime-project file refuses to pick up on changes. I'll take a further look and see if I come up with anything, but maybe this gives you a lead as to what could be happening here?
This doesn't explain configuration changes not being picked up either, but that could be a symlink issue (even though it used to work fine?).
Update: I have my old projects set to use the path of "./", so it works in both Windows and OS X. This seems to be causing the issue for me. Changing this to "." fixes the issue (and works on windows as well).
Update2: Seems the trailing slash is the problem. Same happens with my other projects that use a non-pwd relative path as well. I would say it's probably a good move to trim this slash at an application level to avoid this.