I may not know what I am talking about, but it almost sounds like the game and hammer do not know where to look for the textures when the map loads. You say you have reinstalled. I had a problem sort of like this before with hammer but with TF2. I ended up not only uninstalling local files, but also going in and deleting the folders for that game and in SDK as well. I was able to reload all the stuff via Steam. I have to admit Steam does have a excellent recover ability.

CSS uses a lot of textures that other games also use, like HL2. It might go better if you just deleted every thing EXCEPT maps, sprays, sounds and things you have made. You will want to copy them to a separate folder to place back after.

This way the game had to make brand new paths and not use any previous data when looking for textures, maps, etc.

BE WARNED, this will take a long time to get all the games back to normal. BE EXTRA WARNED, only do this as a last ditch effort. BE UBER WARNED I take no responsibility if you destroy things you have created, saved files, configurations etc. All that MUST be saved to a separate location and placed back if you want to keep it.

If that does not work, I am sorry I have no other ideas.

Don't use the run map after compile option. Let the map compile, then run it manually.