I know exactly what you're talking about, and that is another reason that I struggle to make myself use it. That said, if someone here posts a particularly awesome way to organize the panels, and it extends the feature set in a highly usable way, then it would be worth pressing JRiver to address the random switching of the active Split panel.
On the other hand, if there is virtually no feedback for good ways to use it, then that would lead me down another path. I have been experimenting with some other media players just to see the state of play these days, and some of them have some really slick side panel usage. These other players cannot compare to JRiver and most every other aspect, but in this particular area they excel. I've been thinking about how some of that functionality could be incorporated into JRiver by modifying how the split panels work currently.