I've done a little playing around, and here's what I got.
1. A MNS file, loaded in LT first, will not load at all in full. No errors, no messages, nothing. (Although clicking on the "Load" button really fast seems to say something about the MNC file down where the helpstrings appear.)
2. The same MNS file, copied, renamed, and loaded in full first, will load pulldown menus in LT, but acts as if it has no toolbars. The toolbars don't load; nothing shows up in the TOOLBAR command.
This leads me to believe that somehow the two programs compile menu files differently. I can't imagine why this would be. I'm going to try to post the MNS/MNC/MNR files from LT, so someone can test it and see if it's just me.