Just a comment: It really has nothing to do with the specific Linux distribution you are using. It's the desktop environment that is important. Since I had more such glitches that I found increasingly annoying taking into account that I was using a standard Ubuntu which is surely one of the most used distributions these days, I finally decided to make a hard decision last year.
For my new system, I'm using now XUbuntu which comes with Xfce, a very very lightweight desktop environment. In preparation, I had tested several other Ubuntu versions like LUbuntu, KUbuntu, etc. As it turned out, when you have a version that doesn't show a particular bug, it sometimes show a different bug in the front-end (I remember eg that LUbuntu had a completely screwed splash screen).
I'm currently doing fine with XUbuntu, although you have to clearly say that Xfce is lightweight and cannot be compared with a GPU supported Gnome environment. The only issue with Mathematica on Xfce is that rarely, copy and paste doesn't work and you have to try it a second time.