"Not really sure whats up with the cubemaps problem"
I know im like 2 years late, but just sharing information here.
The only way i can get my cubemaps to work after building them ingame is to type retry, this immediatley crashes my hl2.exe to desktop but when i load back in they seem to have worked.
Disconnecting and reloading the map doesnt make them work for me for some reason, anly a retry (then crash) then reload game and map. Strange to say the least.
The joys of hammer and source