Leaving a small gap in your skybox creates a "deliberate leak" and this will significantly speed up your compile time as it ignores the vis and radiosity parts of the compile process.
Your map will look absolutley fine.
This is what you should do just to look at any changes you have made etc.
As for the missing textures...pain in the ass and its quite comon, usualy its because a brush is slightly off the true line of the grid.
There are 1 of 2 ways to rectify this, either try selecting the brush going to grid size 1 then press Ctrl G (this snaps the brush to the grid)
Or just try redoing the problem brush.
Hope some of this nonsence helps eek:
Seere.

Knew it was somin like that, Ive never had the patience to make a map so I didnt know for sure what Cobra was telling me about but he did tell me and I at least got it somewhat right.. happy: