I have the same problem – I’m using SyncTrazor on all my systems. For me it usually happens when I copy pictures from my camera (sometimes around 500 to 1000. As I’m going through the photos I delete the ones I don’t need – that’s when some of the other systems start complaining. I have one server located over a VPN so it doesn’t get the files as fast as the systems on my network. It will give me errors saying it can’t find the file to copy over. The only way I can fix it is to temporarily make my desktop a master and override the errors. Running a rescan on all systems doesn’t seem to work.
I’ve learned to copy all the files from my camera and let all my systems sync completely before I go through and delete/organize – that usually helps. Next time it happens I’ll try to help debug.