After playing with some of the settings for panel sizes, making the Top Bar a border, etc. I haven't found an answer.
I did notice that my two buttons that switch VPs both restore the Tabs. My best hypothesis right now is that the queries use an internally defined VP, which doesn't happen to include the tabs defined in the Top Bar.
Moving the tabs to the left side of Main, they now stay when clicking a tab which runs a Select All list, but not for the Query By Form for a different object. Switching the second query to a Select All, unchecking Use Form, the tabs now stay, when positioned to the left.
Finally, putting the tabs back at the top, they stay when looking at the Select All lists for both objects/tabs.
So, this one is solved, but is there any explanation other than that the QBF code is overriding the Top Bar setting for the VP?