I've been having this issue for quite some time, but I've pretty much just been dealing with it until now.
For whatever reason, having my taskbar set to auto-hide causes issues with MBT where the taskbar becomes visible while MBT is maximized. Not the whole taskbar, just the thin strip that you can see from your desktop when it's set to auto-hide.
I can be browsing MBT just fine, with no visible taskbar strip, and it normally pops up as soon as I hit play on a title, but I believe it also happens from time to time while browsing through my collections. The only way I can get the taskbar to disappear once this happens is to switch MBT to windowed mode, and then maximize it again; you could see how this would get annoying. Especially since it happens about 95% of the time I click "play" to start watching something.
This will also randomly happen while in the middle of watching something, though less frequently than while initially hitting play.
The other issue I'd just like to lump in here, since I think it may be partially related, is that; sometimes when coming out of the MBT screensaver (by pressing a remote button, usually one of the nav buttons), Emby theater loses focus (ie. I can't control it, until I get my mouse and click somewhere on the screen), which is also a major annoyance, since it obviously takes you out of the experience of seamlessly playing media from an HTPC via remote control.
Of course, I could solve at least the first issue (possibly the second, I'm not sure though) by simply not setting my taskbar to auto-hide; but the taskbar ruins the look of my rainmeter skin, so I'd like to not have to do that.
I've noticed some old posts on here with similar issues, I just thought I'd bring it up again, and list my particular issues, in hopes someone might have a fix to it.