FYI
Super simple and you have probably tried, but sometimes it is easy to overlook the basics.
Have you checked the screws are tight on the board?
Have you disassembled the PM3 and inspected solder joins and components etc?
What are your antenna readings? after boot, do the both display as OK
Im guessing fimware mismatch has been ruled out, this is a trick one.
I think what he means is, too close for a ISO card may cause issues, so use distance space to try and get a read on the cards, The Glassies dont have this same issue, so you dont need the same kind of seperation.
Personally I find I have to press quite hard on my implant to get a read, and my implants are not deep.
I know you have probably tried most if not all of this stuff, but you never know, something may work.