I think I might have figured it out, but a question still remains. I switched over to Eclipse Subverse, and had the same problem. I noticed that because of the way I build my project locally, the src folder is outside of the eclipse project root. So neither of the SVN clients can sync anything outside of the project root, because if it is the root, they can't sync anything above that directory. Is there any way around this? or will I have to re-build my workspace from scratch?
EDIT: Just verified it. If I made a new project, and added a src tree, and some files, it worked fine....so is there any work around?