We'd like to try and track down this issue.
Could you turn on logging (see here for how to do this: http://www.red-gate.com/supportcenter/C ... ta_Compare
and send the resulting logs through to me at alice [dot] easey [at] red-gate.com?
Also some snapshots of the source and target database would be great: You can generate these by going to File -> Create Snapshot in the Compare UI. If you're unable to send those through then could you give us a description of what you were comparing/synchronizing instead?