1) Compile your map to maps/foobar.bsp. Do not place it into a different folder yet.
2) Run the map using the console command map foobar.
3) Run buildcubemaps.
3b) Run buildcubemaps for the other light setting. (LDR/HDR)
4) Move maps/foobar.bsp to maps/yourfolder/foobar.bsp.
Now you can run the map using either map yourfolder/foobar or using the Bonus Map interface if you have BNS's set up, and your cubemaps will work.
Caveat Emptor: The above procedure worked for me. If it doesn't work for you, post about it and we'll see where we went wrong.
