I just went in and tried everything I could think of to confuse TH3 or the FCB. The only way I could make it behave as you describe was to mod the sysex so that Value1=000 and Value2=127 - IOW, reversed. I wish you had ControlCenter, this would be so much easier to troubleshoot.
I've attached a screenshot from MIDIOX of what the pedal 6 messages should look like with the original sysex I sent.
I've also attached a modded version of the sysex with the Values reversed.
It makes no sense that Overloud would have changed the way the MIDI ON/OFF functions should work between TH3 and THU, but who knows?
When it comes to MIDI, they're not famous for crystal clear descriptions. Then, none of the amp sim vendors are. But that's a rant for another day.....