I thought something seemed off when I activated my stone arm passive ability at the beginning- it didn't show up on the left side of the screen. It appeared after I cleared floor 1, but none of my "active" abilities are showing up, and I have all the way through Petrify (which is so useful that I don't really want to continue without it). I can get you screenshots if you want, but seriously. Should be easy enough to track down and fix- abilities simply aren't available!
Do you the two small arrows at the left of the skill bar? Try pressing them and see if that makes them appear. The skills bar is at the bottom right of the screen.
Ah, there you go. I've played 120 hrs, of course I know about the skill bar, but I'm used to them automatically appearing after you gain them! Thanks. I can now be a real geologist