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I think it must be the auto syncing when the iPhone app opens that's the problem. If I manually sync the database from the iPhone app after it's open it appears to sync the changes. I may be under the false impression that the loading screen when the iPhone app opens is contacting the server - but perhaps it doesn't? Can anyone confirm?

I think the problems were occuring when I wasn't syncing changes between the two manually. If I make changes on the iPhone app and then forget to sync before using the desktop app I was creating problems. I think some of these issues must have been resolved with the recent update - because I seem to be getting error messages now when the two databases sync at the same time. But it would be good if the error messages were a bit more user friendly - rather than saying it was restoring from the database, it might be a bit easier to know what's going on if it asked which copy of the database you wanted to go with (ie desktop or iPhone).

Anyway, seems to be working quite well now, so I can't complain too much!