You could ask on the independent Roland-Arranger web site. I'm mostly a style guy so I could be way off base. Just a few guesses:

-Did you "freeze" any edits you made with Makeup Tools after recording? When you save the MIDI file out of the E80 you want it to be as standardized as possible.

-The E80-generated file contains SysEx and the Makeup Tools engine doesn't know what to do with it (perhaps you can remove the offending SysEx with a 3rd party MIDI utility?)

-Perhaps the file created by the E80 is a Type 1 SMF, and the Makeup Tools engine only provides its full feature set on a Type 0 SMF? (Third party utilities exist to convert between types.)

Good luck, please let us know the resolution if you find it.