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Contact the support ninjas for help with the window resizing issue. It can be a bit fiddly to get the default window size setting the way you want it. Also, if you are using perspectives, and have set the Restore Layout box for a perspective, it will use the window size that was in use when the perspective was saved. In other words, there are possibilities for why OmniFocus is behaving in this way that are not necessarily indications of there being a program defect; that said, it is impossible from your description to rule out the possibility that you are encountering a program defect.

The "complete group/project when last action completed" bit is somewhat subtle. There's a preference that controls that for the group/project, which you can find in the Inspector. If you change it there, the effect should be immediate. There's also a preference in the OmniFocus preferences which controls whether that setting is on or off for newly created projects/groups. Changing the latter setting has no impact on already existing projects and groups, ONLY on those created after the setting is altered.