Was it fine back when you used v2.8 or have you tried using v2.8 ever since it started happening? I'm only asking so we can rule out direct third-party software involvement.
I started using XMPlayer from 2.8 (stayed on top just fine) and have recently upgraded it to 3.1. 2.8 is the version i use now - it's all too convinient to have player's control panel available no matter what prog i work in. The reason of this post is to attract attention to a thing that looks like a bug to me. If you think it's just random, bad luck for me, but i'll manage.