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Ok I have two Mac's and I am syncing them with a sync database stored on a mounted SMB network share. Both machines are left on 24/7 and so is the file share server. OmniFocus is running the entire time as well.

I get the message "the client xxx.xxx.xxx.xxx has not been recently synchronized" every 24 hours it seems. If these machines are left on shouldn't the syncing be happening automatically?

They both manually sync without any issue.