It seems to be related to multi-monitor setups. If I put the stack view at position 100x100 on the primary monitor, close and re-open, it appears in the same place as expected. If, however, I put it at 100x100 on the second monitor, close and re-open, it appears at 100x100 on the primary monitor.
[Edit] I just had a look at the saved settings, while reproducing the issue. I opened the sim, moved the stack window to the second monitor and then exited. The saved left position was 2225, as it should be. I then opened the sim and immediately closed again. The position saved is now 305. The difference between the two is the resolution of my primary monitor.
I've also looked at the source code, and while I'm not overly familiar with C++, as far as I can tell, the value appears be assigned to StackFrm->Left correctly. Also, the Hardware, Output, and Memory windows are not affected at all, and restore to their previous position.