I've noticed plooms of dirt here and there. The sort that appear when you walk. I know sometimes when someone is stealthed or invis you can see this, but this is not the case. Thye appear in the same places. I've even sen one a but above the air. I dont know if these were put in to keep people on their toes or if this is some weird side effect of making a kick ass server.

No idea.

Yes.

I'm absolutely 100% certain that I've seen this before in numerous places. At first, I thought it was a DM, but they stay in the same place forever.

I'm pretty sure it's just a fault in the Underdark Tileset.

That sounds like a good explaination. It's a feature!