MMM... sausage.
The reason that this happens (the color in the textures thing) is that the textures have their own paletts, or pallets, or something like that... anyways, it forces the texture to use only certaint colors, the best may I have found around this is to open the texture up in paint (really freakin old) and then select all of it, open another new picture in paint with the same deminsions and paste it into the new one, this will remove the pallet, or palett... whatever. The only problem is that paint has trouble saving pictures in 264 bit color, so if the texture is for a HL model (it must be 264 bit color.) copy it into wally, then export it as a bmp. Then you can use it in a model.
I bet there is a simpler way of doing this, but I don't know it.