I removed all the connections from the BNC at the back to all the backplane connectors.
Now everything is fine. Even the DC505A that was not counting anything while on the extender, is now working fine inside the mainframe. I should wire EVERYTHING, every pin on the extender. Even those not dedicated to the power supply of the plugins. I thought I could just get away with wring the first 13 pins, but no. Some plugins (DC5xx) in particular need the others too.
So apparently I had 2 issues, the rest of the pins, AND option 12... Now all is good.
Except my DC503 stopped counting altogether. But I’m posting on the appropriate thread about this.