So once this starts happening, it won't resolve itself after some (short) time? You really have to stop the synchronization? What kind of change are you making? Is there any pattern? Is it easy to reproduce?
We are noticing if we make changes in the local files/folders that are under "Keep remote directory to up to date" at some point we will get permission errors while using explorer.exe to make changes. We have several hundred directories that are being monitored. Is this a "known issue"? Obvious work around is to stop the operation, then restart it after making changes but of course we'd prefer to keep the synchronization going 7x24. Seems to happen if user access folder via network share or locally - all specified users have Full permission access to the directory being synched.