I've had the same thing happen with me, and to be honest it frustrated me to the point that I didn't want to learn how to mesh anymore earlier this year... and it's exactly why I'm sticking with Blender3D from now on. It's cool and everything, especially with all the neat plug-ins that Wes_h made for it involving animation and such... but ever since they changed or screwed around with some things in the newer versions of Milkshape (
*coughfreetrialperiodcough*) It hasn't been very friendly at all on my meshing experience, and sometimes I even think it confused itself after registration (yeah, I actually gave in to purchasing a license it)... since the "NOT REGISTERED" line in the title bar never really went away after my first few tries with 1.8.2 and the free trial was nil. Even after I deleted it and installed a different version it still didn't work and the messages telling me that I seemed to have "registered the copy after it expired" wouldn't go away. So now it's sitting in my recycle bin, still waiting for the next disk clean-up I do for my laptop. [/sad sob story]
Of course, people around the community have had better luck with Milkshape, so I'm not saying that it's a complete bust overall... just for me personally. Maybe someone who knows more about it can offer some advice on how to get it working for you again.