I've figured a way to export from milkshape to blender, and then to Quake
You experience it as buggy. Why don't you use a mdl.editor that catches *.md2 files and sends them out to *.mdl?
Sorry for Milkshape, but it lacks this feather. Lots of other extentions, but no quake1.
Here is one:
This one imports and exports mdl and md2 simultaniously.
So now that's a better way to import your q1 models into Milkshape. You say you want to stick with Milkshape. That is your own choice, if you are familiar with it.
Now the other way around. You want the milkshape ms3d file turned into a quake1 mdl file?
First thing I would think of is to export it to a q2 md2 file and import it in the q2mdl editor above. Then export it back to q1 mdl format.
So far your question. There are more quake mdl editors. Misfits is a free model editor and has a lot more import extentions, than the only ms3d of Milkshape.