I've having some serious issues with this place. At first the tower was invisible, I mean completely, I couldn't walk where the tower was suppose to be due to an invisible wall...but it was actually the tower. Now that I have finally gotten it to appear the door the quest marker is pointing to is invisible.

Have you exited it from within Blackreach? I've only recently poked around in Blackreach, but I got the impression that we have to exit from within Blackreach before we can enter it from Skyrim. ...or, worse yet, are you trying to enter it from within Blackreach?

No, I can't even enter the tower of mzark. I'm not really sure what you're asking.

Sounds like missing/misplaced textures and environmental stuff. Happened to be in Whiterun. An entire portion of the floor was missing. Some suggestions:

• Exit Blackreach via lift. There are many scattered around, you just have to look for them.
  
• Save the game while outside and reload
  
• Turn your 360 off and clear the cache
  
• Try downloading Skyrim to your HDD. That may have an effect.

Just remember to do all of this with a save OUTSIDE of Blackreach. That should reset the area. Granted, these may work while inside as well.

Are you IN Blackreach? If so, that's apparently a bug of some sort. If you aren't IN Blackreach, it doesn't matter if you can find the tower or not, because you can't get INTO it from Skyrim outside, you have to be down inside Blackreach.

You have to enter Blackreach (long ass trip) via Alftand. Then, once you make it to Blackreach you have to enter the bottom of the Tower of Mzark. An elevator will take you to the surface of Skyrim. After you've done this then you can enter Blackreack from the top of the tower which is in Skyrim proper.

I thought that the entirety of Mzark was actually underground?

Might be - I've only been to Blackreach twice and didn't spend too much time there, but there's a tower that has the base in Blackreach and the top exits in the mountains waayyy southwest of the Alftand entrance. I was f-ing shocked when I saw it on the map when I exited from the tower.

Edit: I think the distance between the Alftand entrance and Tower of Mzark exit are greater than the distance between Whiterun and Riverwood.