Make sure you have a light_environment in the level. Also, it might be worth moving the whole map into another .vmf file and trying to recompile that. It may fix the "black blotches" issue. I had something similar before.
Heres a link to the thread I posted a while ago when I was having the same issue as you, might be of use:
@rocky Do you have a 3D Skybox ?
Any object in the 3D Skybox that cast shadows will have its shadow projected from the 3D Skybox to the map. I just made a drawing to show what exactly it means :
[Blocked Image: http://i.imgur.com/F6wNnsH.png]
Therefore, if your 3D Skybox is not properly placed, an object could cast a huge shadow on your map.
Or maybe as Plat said there's just no light_environment ... 
that is is a NICE drawing 
could also be fog settings
inb4 forgot to check the light entities in the visgroup.
Send your compile log m8
(More seriously, could be a T-Junc error)
Could also be some light entity inside basic brush.
Compile log over pastebin or something would be very helpfull.
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