Whenever there's water I was seeing stuff like this:

I found the opengl shader setting that says to turn it off if you're having graphics issues. With it off I got this (with show grid turned off):

Much better even though I didn't want a grid, but unfortunately turning that setting off also messed up the level up screen somehow:

So I had to turn that setting back on again.
It only seems to affect areas where there's water for some reason.
Everywhere there isn't water ToME looks just like it's supposed to, so it doesn't make the game unplayable or anything.
Only serious issue it's caused is that it actually made a town invisible, so it was a bit lucky that I actually found it.
(Last Hope is the tile right underneath that patrol near the graveyard):
