I figured out why.
Key thing I noticed was that sometimes they stacked, sometimes not.
What you said about the Main windows always stacking was the clincher.
The reason my MCs don't always stack is that I'm frequently launching them with different parameters specifying different .ini files. If I launch multiple MCs with the same parameters, they stack as expected, but in their own stack which is different than the Main window stack.
Not the behavior I would want from Microsoft.
Sorry to have bothered you with this non-problem.