I have discovered that my clippings and notes are not syncing between my two computers. It could be something simple as a setting or a bug that is not allowing the syncing. I create a clipping or a note on one computer and it is not showing up on my other computer.
You must have the Tools -> Program Settings -> Use Internet set to Yes on both machines. If this is set and you still don't see documents syncing please post a log file from both machines.
http://wiki.logos.com/Diagnostic_Logging