Okay, not sure what's causing this, but I was able to track down that it only seems to happen with Random Psideas enabled. I downloaded version 1.2.1 of the Omnifactory pack. I installed Psi 1.1-77 and Random Psideas 2.4.2. When I hit F7 to see the light level overlays, they're no longer colored, they come out white/light grey instead of green/red. Also when I use the Scannable scanner to scan for ores they also come out colorless. When I disable Random Psideas, everything is correctly colored again.

Edit: Okay, never mind maybe, it also seems to do it with a few other mods I tried to install. It might have nothing to do with this mod. It's kind of frustrating as I can't track down what's causing it. I think I found a thread about it, but they seem to say it's something that comes and goes.

Edit2: Okay, I fully restarted the game and now it's working right, this is very strange.