As the only way I can uncheck a folder is to wait until it is backed up, it creates issues for whenever I don't want it sync'd (like the subfolder with all my picasa photos)
1. Start sync'ing
2. notice that it is sync'ing a folder you want to ignore
3. go into preferences and uncheck it.
4. Go into Google docs and move it in the trash
5. after syncdocs gets going again, watch it reappear.