I have the same or a similar issue. It can be readily reproduced. I'm using patch 1.17a. I did not notice it on 1.15x or a few of the early 1.16x patches.
I have a stack with multiple entities (brigades, divisions, leaders, etc). The stack is OUTSIDE (either afloat or not in a structure on land). If I select one or more of the entities in the stack and drag it on to the stack itself, creating a new stack outside in the same region, it will represent that stack visually down a few regions. I can click and drag the stack back up to the region it says it's actually in with no issues. I can do any normal operation to the visually misplaced stack and there are no errors. The only thing I can find wrong is where it drops the new stack. It doesn't happen if I select the units and instead of dropping them on the parent stack, I drop them on the unoccupied land in the region somewhere.
It's been annoying but I've been dealing with it. I had it happen on both Windows XP and Windows 7. I'm willing to be shown that it's something in my installation, but you're going to have to do a significant amount of work to prove it to me.