Maybe you're forcing some older version of DirectX? Possible driver problem? I know NVIDIA F'd up my flashbang effect a few months ago and it was just about giving me seizures. Luckily that's fixed.
forceing the game torun in DX8 will make those windows completely transparent. if this happens every time then redownload the map it should fix any texture isues
shotgun runs a very nice Aids anon meeting twice a week. hes helped many a TD member with this epidemic.
but ya try deleteing and reinstaling the map file if that dosnt work do the same for CS if that dosnt work do GFX drivers then DX if none of thaat works enjoy your black windows