Have you tried removing TC from the Startup? Or removing it in the msconfig utility in the Startup tab?
As I've told you, I don't know much about texturing, but I do know how the game engine handles them. Maybe MoreDread or TodeswolF might be better at helping you choosing a suitable program.
I still think Photoshop with the DDS plugin is the best way to go, it handles mip-maps without any problems. You can just generate new ones when you save your edited files. I made 2 new uniforms and added the shoulder patch you made on one of them.
Here's anotherone I made, but it'll get changed once I have some new camo patterns to put on it.
I uploaded the pack for anyone that's interested, just PM me or join the chat at Mibbit and I'll explain which files to edit to change the model skin.