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We've tracked down the slow sync problem, and fixed it for the upcoming 1.0.3 release.

For the curious, the problem is triggered by a large number of transaction files: OmniFocus was trying to traverse the antecedent transactions for each transaction to figure out which transactions it needed to download from the server, and ended up in a Towers of Hanoi-like algorithm where every additional transaction made the process take nearly twice as long because we would revisit all the previous work yet again when looking at the new transaction.

The solution in 1.0.3 is to fix the algorithm to only look at each transaction once (which is how we meant for it to work in the first place), but a workaround you can apply now is to reduce the number of transactions by making sure each sync client connects on a regular basis (which lets OmniFocus clean up old transactions that it was only preserving in order to let out-of-date clients catch up). I guess that's why I hadn't seen this myself, yet; all my clients were connecting on a regular basis.