Sounds like a poor install, try reinstalling the game.

I've had no issues with transparent items or pet limbs. Though there was a thread with a switch on a wall now showing up for a few people and they reinstalled the game which fixed it. After reinstalling the game, install the patch again.

Every time there I run into trouble on the road, there is always a dwarf at the bottom of it. Don't they know how to drive above ground?