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It sounds like OmniFocus is starting in its Default View. If you go to Perspectives -> Revert to Default View, does OmniFocus show the same view you see when starting up (i.e. the one focused on a particular project)?

You can save the Default View by first doing the Perspectives -> Revert to Default View thing, then set things up as you like, and then quit OmniFocus. When you reopen the app, the Default View should be preserved as you last had it.

On my system, any perspective I had set when I quit OmniFocus is displayed again when I relaunch the app. Does that not work on your machine? Note that I don't have mine set to open automatically as a login item; I just launch OmniFocus manually and leave it running all the time.

-Dennis