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Does it ever happen if OF has been running for less than a day? You might try quitting and restarting OF every night while you are asleep and see if that at least masks the problem. You could do this by running a script from iCal that just tells OmniFocus to quit and then tells it to run.

I run OF pretty close to continuously on my machines, although it does get put to sleep now and then (mostly when I move the laptop) and I tend to reboot often enough that running for more than 24 hours on the primary machine is a bit unusual. I've never seen the behavior you report, but it also isn't clear to me that it might not be affected by which views you use. I'm almost always using a window that groups by either start or due.