I recently purchased a second hand Ground Control and Gcx system.Since you've already tried resetting the Ground Control to the Factory Default settings along with double checking each Instant Access button to make sure the loop assignments are correct, I would suspect there is something internally wrong with your GCX if the same problem still exists.
I have reset the Ground Control to factory settings. The Ground control is being powered by the Gcx. The Gcx is hooked up to my amp effects send / return thru the Feed thru input and then I have connected the feed thru into the 1st loop input. Then hooked up all loops.
On a trial I set up the ground control to the mode where pedals 1-8 turn on their corresponding loops. Loops 1 - 4 work fine. But when i tried loop 5 - even tho loop 5 lit up on the Gcx - it was turning on the loop 6 pedal. Similarly pedal 6 lit up loop 6 on the gcx but the pedal from loop 7 turned on.
I tried wiring each loop up individually - so - for example - feed thru into the input for loop 2, send and return thru the pedal and then output to amp. Each channel worked fine - but loop 5 did nothing, and then if i hooked up loop 6 - pedal 5 would turn on that loop even tho the light on the gcx still said 5.
My hunch is that something in loop 5 on the gcx has become disconnected in transit (or the seller is lying).
But i would like to hear if perhaps I'm doing something obviously wrong - or if anyone has any ideas what might be happening internally before i have it looked at. I also - after resetting, went into utilities on the ground control to see if the pedals were definitely triggering the right loops and it seems so.
By the way, you can directly connect your amplifier's FX Send to the Input jack of any GCX Loop; there's really no need to use the Feed Thru.