Oh
deer. So many errors in this. I am fixing them as we speak. I'll edit this later with an explanation and a download link.
EDIT: For this test, I switched to software if you're wondering.
Okay, so I tried a couple of things. First, I pressed F4 and found an error. On the bottom left of the map, I found 2 open sectors, so I closed them to prevent visual bugs and other nastiness. I hen tried to draw lines around the places that looked like deleted sectors (quite a LOT D:) to see if that would fix it, but nope. Then I deleted the tower by Sector delete, then deleted it's remaining lines. And it worked. No more glitched skies. I mad ea new sector with a tag number of 3 to see if it worked, and the bug returned. I closed many sectors around it too, and it persisted. This is beyond my understanding, but I would suggest that you refrain from building anything in that area.
Your map was missing a MAPINFO lump, which is needed in every map, so I took the liberty of adding one. You can change the music in SLumpED. (I put SDEMUS, Shademan's theme.)
This map, by the way, has some cool new textures and sprites. Well done! Here you go:
http://www.mediafire.com/?9sdfa6wbw2hl3il