The error message appears once at every startup in a dialog box. In the log file there are only one warning (unrelated, I suppose, looks like a duplicated class in framework)
04/03/13 10:09:19,206 DEVONthink Pro[421]: objc[421]: Class CJSONDeserializer is implemented in both /Applications/DEVONthink Pro.app/Contents/Frameworks/DEVONappkit.framework/Versions/B/DEVONappkit and /Applications/DEVONthink Pro.app/Contents/PlugIns/Sync.bundle/Contents/MacOS/Sync. One of the two will be used. Which one is undefined.
Databases are local, in ˜/Document/MyDatabases folder, then synced via DropBox