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Have you worked the issue with the support ninjas?

If the issue is that the app takes too long to start when you pull the iPhone out of your pocket to make a quick note of something, why not turn off Auto-sync? Then the app will only sync when you direct it to do so, at a time of your choosing. You can make your entry, start the sync and then push the sleep/wake button on the top of the iPhone to prevent any accidental input when you put it back in your pocket -- the sync will continue.

Another way to help keep database size and sync time down is to get your devices synced up whenever you switch from using one to the other. Don't make simultaneous changes on desktop and iPhone if you can avoid it, but rather use one, then sync both devices before switching to the other. It's easier if two people take turns editing a document, right? Same applies here, it's much harder to keep the changes straight if both people are making changes to a document simultaneously. It's also easier to get duplicates in your database if you are completing repeating actions in two places.