As far as I understand having more than one window open at a time is not what the issue is here. However, view configuration should be done with a single window open; after that multiple window can be open without OmniFocus having to address possible conflicting parameters of a single perspective's view. When you are switching between Project and Context views; you are essentially changing perspectives in OmniFocus. To address the problem you need to do a few things.
- Choose your "Projects" view and set it up as you like.
- Select in the menu bar Perspectives > Take Snapshot of Projects.
- Select in the menu bar Perspectives > Show Perspectives (Control-Command-P).
- The perspectives window will open with the "Projects" perspective highlighted.
- Select the aspects of the view you wish to be restored under the restore heading. These include; Focus, Layout, Expansion, Selection, and you can pull settings from another perspective.
Additionally, you should notice you can have a perspective always open in a new window.
The process is similar to change the "Contexts" perspective and/or any other default or custom perspective you utilize in OmniFocus. Notice the "Take Snapshot" menu bar item is dynamic and will change to which ever perspective OmniFocus is currently using.
