I can't say what's going wrong on your end, but you could try using a different tool to extract the graphics.
My level viewer should be able to load the graphics of most mods. Once the levels have been loaded into that program, you can press F4 to export all the graphics (tilesets, sprites etc.) as PNG images.
I tested it on a copy of UCK4 I had on my harddisk and it worked, but I might have hacked my version of the mod so that I can use my tools on it.
Edit: It would be a lot easier if Gommander Genius had an option to export the tileset graphics for you. If CG supports the game/mod, it is obviously able to load the (modded) graphics from the EGAGRAPH file. It would only require a few lines of code to make the CG export the graphics in a format that can be edited with somewhat modern tools.