Unfortunately issue #19 seems to be back again, I would've added this onto that one if it wasn't closed and locked. Currently running 1.12.2-1.0.15-b2, but first encountered on 1.12.2-1.0.15-b1.

Thx for filing, this is a quite tricky one that I am not able to reproduce. The windows are rendered using the combined transparent/solid rendering available in Forge, it is possible that BF somehow renders as "overlay" (or so) in one of these. If I recall correctly mipping had a role in this.
Could you check your graphic settings, if the mipmap level is 1 or higher (not 0)?

Ah yes mipping is indeed playing a part, I had it on 0 when I was having the issue, anything higher than that works correctly.

Ok so we have at least a workaround.