I use a combination of Performances, Songs and Patterns for “live” performance. Of the Songs, many are based on MIDI files that I edited, re-recording some parts, leaving others. And I’m very careful about going through each track to find and remove EXC events and things like that, which can really mess with you. 

I have one particular Song based on a commercial MIDI file that seems to always add a huge amount of Reverb/Delay or possibly it’s changing the type of Reverb/Delay or something as soon as I hit Play. I have gone through all the events on all the tracks and removed extraneous stuff, Volume, PC, Expression. I don’t see any event in any track that would be calling for a certain Reverb/Delay/Chorus to be selected, but it sure seems like that’s what’s happening.

Is there any way certain MIDI events in one of the tracks is STILL sending a command somehow to the FX block on the MOXF?

My preference would be that the main “FOH” mix and effects be the same from one Song/Pattern/Performance to the next. Do Master or System FX have a default go-to FX setting? Where would I look when comparing this one Song to another Song that sounds more “normal” to me?  (Six years later and I’m still quite vague on the practical difference between System and Master FX.)

For now, I’ve taken to turning off the Master Effects when I come to that Song, but I’d rather not be fiddling with those buttons EVER in the course of my live show.

Without seeing the specific MIDI file, it’s somewhat difficult to determine what it is you’re experiencing. However, even if you’ve removed any Universal SysEx Reverb and Chorus messages, you should be aware that GM Level 2 files can include certain Control Change messages, such as Reverb Send Level (CC#91) and Chorus Send Level (CC#93) - the Motif family does respond to those.