The version now up on the website (r5879 or better) should use slightly different background colours for covered and uncovered squares. I found it looked really weird if I made them any more different, but I hope it's helpful anyway.

Have you had any more trouble with instakills or guessing?

I've just been playing r5936, which seems not to be having problems with instakills. I don't know whether it's just my computer, but I'm really not seeing any difference in the colours of covered and uncovered tiles. Looking at the M$ minesweeper, I notice that the covered and uncovered tiles are uniformly a medium grey, but that the uncovered tiles are framed more strongly than in your version. Possibly it's this difference which is confusing me.