Thanks to MrBlip for his suggestion, after removing the door and then fiddling with the brushes (mostly with how they were alligned) something clicked and it worked.
As for the black walls, if the texture was the problem then the entire inside of the warehouse, and the other two I've made would be as well. It's only small sections, and I can't see what makes those sections different from the rest.
If it were the prop shadow issue that NightSnipe linked, then I can't see what props are causing that. The only props nearby that are large enough are the shelves which are on the other side of the warehouse.
I'm gonna grab a Compile Log in just a second.
EDIT: Here. (VVIS was set to Fast so it wouldn't take too long.)
** Executing...
** Command: "c:\program files (x86)\valve\steam\steamapps\n05k1ll2\sourcesdk\bin\ep1\bin\vbsp.exe"
** Parameters: -game "c:\program files (x86)\valve\steam\steamapps\n05k1ll2\counter-strike source\cstrike" "C:\Program Files (x86)\Valve\Steam\SteamApps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimited_v1"
Valve Software - vbsp.exe (Dec 11 2006)
2 threads
materialPath: c:\program files (x86)\valve\steam\steamapps\n05k1ll2\counter-strike source\cstrike\materials
Loading C:\Program Files (x86)\Valve\Steam\SteamApps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimitedv1.vmf
"materials/dev/devwindowportal.vtf": cached version doesn't exist
fixing up envcubemap materials on brush sides...
Material glass/glasswindowbreak070b is depending on itself through materialvar $crackmaterial! Ignoring...
envcubemap pointing at deleted brushside near (1408, 1728, 256)
Material glass/glasswindowbreak070b is depending on itself through materialvar $crackmaterial! Ignoring...
Material glass/glasswindowbreak070b is depending on itself through materialvar $crackmaterial! Ignoring...
ProcessBlockThread: 0...1...2...3...4...5...6...7...8...9...10 (0)
ProcessBlockThread: 0...1...2...3...4...5...6...7...8...9...10 (1)
Processing areas...done (0)
Building Faces...done (0)
Chop Details...done (0)
Find Visible Detail Sides...
Merged 732 detail faces...done (0)
Merging details...done (0)
FixTjuncs...
PruneNodes...
WriteBSP...
NODRAW on terrain surface!
NODRAW on terrain surface!
NODRAW on terrain surface!
NODRAW on terrain surface!
NODRAW on terrain surface!
done (1)
writing C:\Program Files (x86)\Valve\Steam\SteamApps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimitedv1.prt...done (1)
Creating default cubemaps for envcubemap using skybox materials:
skybox/skyday01_06*.vmt
Run buildcubemaps in the engine to get the correct cube maps.
No such variable "$hdrbasetexture" for material "skybox/skyday0106rt"
Can't load skybox file skybox/skyday0106 to build the default cubemap!
Finding displacement neighbors...
Finding lightmap sample positions...
Displacement Alpha : 0...1...2...3...4...5...6...7...8...9...10
Building Physics collision data...
done (1) (704548 bytes)
Placing detail props : 0...1...2...3...4...5...6...7...8...9...10
Compacting texture/material tables...
Reduced 3657 texinfos to 1990
Reduced 251 texdatas to 218 (11185 bytes to 9557)
Writing C:\Program Files (x86)\Valve\Steam\SteamApps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimited_v1.bsp
11 seconds elapsed
** Executing...
** Command: "c:\program files (x86)\valve\steam\steamapps\n05k1ll2\sourcesdk\bin\ep1\bin\vvis.exe"
** Parameters: -game "c:\program files (x86)\valve\steam\steamapps\n05k1ll2\counter-strike source\cstrike" -fast "C:\Program Files (x86)\Valve\Steam\SteamApps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimited_v1"
Valve Software - vvis.exe (Nov 8 2007)
fastvis = true
2 threads
reading c:\program files (x86)\valve\steam\steamapps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimitedv1.bsp
reading c:\program files (x86)\valve\steam\steamapps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimitedv1.prt
1983 portalclusters
6212 numportals
BasePortalVis: 0...1...2...3...4...5...6...7...8...9...10 (13)
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
WARNING: Cluster portals saw into cluster
Optimized: 182829 visible clusters (0.00%)
Total clusters visible: 2998171
Average clusters visible: 1511
Building PAS...
Average clusters audible: 1932
visdatasize:968734 compressed from 983568
writing c:\program files (x86)\valve\steam\steamapps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimited_v1.bsp
13 seconds elapsed
** Executing...
** Command: "c:\program files (x86)\valve\steam\steamapps\n05k1ll2\sourcesdk\bin\ep1\bin\vrad.exe"
** Parameters: -game "c:\program files (x86)\valve\steam\steamapps\n05k1ll2\counter-strike source\cstrike" "C:\Program Files (x86)\Valve\Steam\SteamApps\n05k1ll2\sourcesdkcontent\cstrike\mapsrc\cscompoundunlimited_v1"
Valve Software - vrad.exe SSE (Nov 8 2007)
----- Radiosity Simulator ----
2 threads
[Reading texlights from 'lights.rad']
[1 texlights parsed from 'lights.rad']