I'm having the same problem on 100% GUI - I can't yet pinpoint the exact cause of the glitch, but occasionally a vertical scroll bar will appear in the middle of the screen (it's possibly caused by tabbing out of the game, but I'll add more details if I can narrow it down).
I have quite a few mods loaded (one of which may be contributing to the problem), so without knowing which one caused the problem I've been solving it by saving/remove all mods/save/enable mods/load, so it's nice to know that there's a shorter workaround (without losing mod settings) :)