I had a problem very similar to this with the same error message. The issue was being caused by my Dropbox settings in TR. Turns out that I was pointing to the wrong directory in Dropbox. I resolved the issue by correcting the information in TR. If you have not done so already, please go to Tools > Options > Miscellaneous > iPhone Sync
Ensure the Dropbox option is selected and that the directory is pointing to the your local dropbox folder and no deeper. For example,
"C:\Documents and Settings(slash)Administrator(slash)My Documents(slash)My Dropbox"
I hope this resolves the issues!