Yes, I have noticed this too. Happens especially when resources get scarce. It's sad that this problem is still ongoing after all these years and releases.

My workaround is to create a sorted list in a project sub-group. This one you can then completely close and reopen, which opens them in the same order as listed there then. However sometimes this list looses its order for some reason too, less frequently though than the windows list.

This messed up window list sort order problem exists as well in the latest version v12.0.2.1818. I managed to create a test case.
The problem always seems to occur when the list of items in the window list gets long enough so that you need to scroll and when you change the order of the windows in the window list then. The same behaviour can be reproduced as well with v11.0.6.1776.
I will send the test case details with screen shots via e-mail.

Were you able to reproduce the problem using my test case? What is the current status of this problem now?

Marco, could you please respond?!
After all this is really an ancient problem waiting so long to be finally fixed. This is also why this thread has the 2nd most views of all.

Marco???