Mark IV effects loop switching - nasal/out-of-phase sound

I ran into an issue with the remote switching of the effects loop on the Mark IV. With the FU-3 switcher disconnected and all remote jacks connected to my old midi switcher the effects loop goes out of phase (or so it sounds) when set to full power on the front panel - but not when it's changed to "Tweed Power". This is with any patch engaged on an Eventide H9. When the effects loop is turned on permanently, it's normal in both power settings. Everything is fine also when the FU-3 is plugged in and the hardware switch for the loop is set to off.

I'm sure I'm not describing this to easily follow. It's late, I've been messing around with everything I could come up with (changed a tube for the effects loop already), and I have 2 practices and 3 gigs coming up in the next few days that I wanted to use this amp for. Which I can if I leave the effects loop on via the switch in the back of the amp. Doesn't make the difference really if the selector is set to "footswitch" or "external". Same "out of phase" issue with the loop engaged in Full Power mode.

Just trying to figure out what this is and what can be done. I definitely need midi channel switching and the EQ on/off. If the remote/external jacks don't work like this I may have to buy the "amp gizmo" with the designated Mark IV cable that connects to the footswitch jack. Which would suck since they ain't cheap and I thought I had already what's needed.

Update:

At around 2am I realized that having all three channel switching 1/4 cables plugged into the Mark IV (rev B) seems to cause this. When I only put in the cables for channel switching on yellow and orange while setting the mode dial to "foot switch" instead of "ex switch".

I may have read here before that the layout of that circuitry is a bit wonky. Can anyone confirm this observation or am I still doing it wrong?