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To close the loop (at least for me) on this issue, I can advise that I communicated with Omni Support via email, providing iPhone console logs, etc.

Firstly, Omni support were terrific.

Secondly, no clear fault could be identified other than geographical distance between me in Perth, Australia and the OmniSyncServer in Seattle. To be fair, this is basically opposite sides of the globe.

I have used the Sync Server since it was launched, so have always presumed that my sync speed was normal.

However, to test it I created my own WebDAV sync on my NAS. Now, sync is so fast - even when routed through the Internet, and not through the LAN - and I haven't had any freezes.

I should have done this sooner!