pic32prog with pged3/pgcd3 not working

[tsupplis]

I found a strange scenario: I am using the pinguino-mx220 board of olimex. Using the ISP connector with a pickit2, the target is not found. the ISP connector uses pged3/pgec3. If I connect the pickit to the pged1/pgec1 pins, i.e. bypassing the ISP connector, it works without any issues and the target is perfectly recognized.
In parallel, I used pickit3 and mlabx to program the mx220 using the ISP connector and it works perfectly.
Trying to debug further seems difficult. is it pickit2 struggling with pged3/pgcd3 or is there a limitation in pic32prog? Any suggestion on how to debug further?

A pointer to the schematics of the board:
https://www.olimex.com/Products/Duino/PIC32/PIC32-PINGUINO-MX220/