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Turns out it was a corrupt OmniFocus file. After I installed the app on a new machine and set sync in the preferences for a new blank default OF document, everything worked as expected.

I therefore went back to the original machine and master file and ran the various routines for fixing the file. This file began life in the OF Beta last year. My backups were 40k and the original file was 21mb, an indicator to me of an inherent issue with the file.

After running the "rebuild" and the "CoalesceDatabase.scpt", I still wasn't getting any joy with the sync. So I created a new file and re-imported my data via a revert to back-up - I think!! (This process is rather non intuitive). Suffice it to say, I got all my data back in.

Success. Seems like all is working fine. Thanks for the pointers.