On the heels of the last post, another issue I ran into was with the remoting and web service classes. These are not included as external .as files at all, but are pulled into the swf in the swcs you put in your library. Thus, there is no way for mtasc to get at them.
The solution I came up with was to drag the remoting and web service swcs into a new fla, and publish it as a swf. Then I used ASV to decompile the swf. I then went to the ActionScripts tag and could see each class listed. Highlight each one and hit F12 to save it in the appropriate directory in your mx class path. Voila! Perfect compilation.