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Fireproof, crashes shouldn't cause a problem with the sync process - it's designed in such a manner that unexpectedly quitting the sync early doesn't cause problems. It just picks up where it left off next time it syncs. (If your crash reports were sent in and you'd like the support ninja to have a look at them, they'll be happy to do so.)

That said, if you open the Sync prefs on your Mac and press the "Show Clients" button, how many entries appear in that list, and what's the earliest "Last Synced" date?

As Bill mentioned, changes create new zip files. In addition to changes you make yourself, changes the software does on it's own will also create zip files. (Examples: when an action goes from unavailable to available, or from due soon to overdue.)

In general, any files that both the Mac and iPhone know about should go away if they're at least an hour old. It's possible that those zip files are just being created very quickly as you move stuff around and settle in to OmniFocus.

I don't think you're seeing a number of files that are way out of line with normal but if you see the number of files go up and up without ever getting smaller, let us know and we're happy to investigate.

As to sync times, some of it is undoubtedly the phone, but if the server is just taking a while to respond, that's not something we can address in the app. It's not uncommon for me to see sync times like that when I sync with my iDisk, for example.