I figured it out. I was creating automation loops for each effect Loop. The issue is that CC's in MIDI are serial commands, they cannot overlap, or you get problems. The best solution was to create a very short automation loop with basically a single data point, not a running line of ON/OFF setting like I had been doing. Then when you want Loop 4 Off and Loop 7 On for a measure, you make sure the commands are spaced apart by the smallest increment possible. This cleans up the MIDI signal.
This has been a ton of trial and error, and yes, using MIDI-Ox does help with the troubleshooting. As a guitarist I waded into this knowing little about MIDI and have learned quite a bit. If anyone wants to explore this it is a great way to automate your pedal changes, as long as you either are playing to backing tracks or willing to commit your drummer to a click track.
Here is my set-up and how it now works:
Bandhelper App on iPad> Mastermind PBC> MIDI Capable Guitar Pedals (including a MIDI capable Infinity Looper)> Roland Basspedals> Kronos Keyboard
When I select a song on Bandhelper it can either play a click track or a Backing track, depending on my preference (one setting in Bandhelper can be changed to choose between the Backing Track or a second recording with a custom click. Bandhelper does provide its own click track, but the custom click recording allows better options such as a different click to cue when to start the song, or perhaps a louder click on the "one")
The MIDI file is attached to each recording and automates changes in loop settings. Unfortunately PC changes, which would change Presets within a song, are only one time things for MIDI files at the beginning, so You cannot automate changing Presets during the song with a MIDI file, but you can turn loops on and off, which involved CC commands. I create the Automation loops to control these changes in FL Studio and export the MIDI file into Bandhelper. In addition to controlling my Mastermind and automating it, I can control my Infinity Looper pedal to get absolute Loop accuracy. This was the MAIN reason i went to MIDI file automation. I had already gone to MIDI SYNC with a click track, but there was still instances of occasional Looping erros...millisecond delay in hitting Start or Stop on the looper can result in the loop not triggering until the next measure and being off. By programming the CC in on a sequencer I no longer have to worry about trying to hit the buttons just a moment early, which is very distracting to performance.
I cannot issue Preset cahnges to the other MIDI enabled pedals using the MIDI File, as again these are PC messages, though I could send CC's for changing individual parameters. An alternative that Bandhelper offers is its own Automation, which you can set up to change Presets within Bandhelper automatically. The reason I skipped on that for everything else is that it is time based, and while you can tweak it to milli seconds within the app, using a sequencer is WAY more accurate for CC's, especially with looping.
Finally, I also play my Basspedals for backing Bass and synth stuff. Automating the Preset changes has made that job a LOT easier. Technically I could automate the notes for the Basspedals or just reocrd that into backing tracks, but I am trying to maintain some "real" aspects of the performance on principle.