I can confirm this too on ZDoom/Linux r3239 (and a fresh compile of GZDoom).
I noticed that third first-level run-through I did, the way to the first key room was fine, but on the way back from the key room, lots of sectors in the large room at the beginning had become dark.
With the GZDoom tests, every run seemed fine (I did 3 here also), until you start a new game without exiting, then BAM. Dark sectors all over the place. In the last GZDoom test, I saw lots of sectors go dark right before my eyes when doing things like hitting triplines and switches.
I tested in r3224 and was able to find some black/dark sectors. I tried in r3222 and after 5 games I did not find any. The random nature of the bug means this isn't a definite but my guess is that my hunch about the light values outwith 0-255 change in r3223 (which I don't have a build of) being responsible may be correct.
Since it hasn't been explicitly mentioned, also know that this only happens in Hexen. Doom, Heretic, and the others are fine. For me, that is, but it seems to be the same for everyone.