Hi,
Firstly, thank you for all the hardwork developing this programmer!
I have a similar (ish) problem to #6 with a hand soldered pcb.
When using easypdkprog probe, It responds with no MCU found (PFS-154C in the socket).
Using easypdkprogtest, it only gets to 3.46v for vdd and 3.44v for vpp. I've confirmed these values with a multimeter. Voltage around the diodes is identical to Paul - (-2.7v D3<->GND, and 0.0v D2<->GND, -1.5v<->GND for both diodes on the shared side).
If I change easypdkprogtest to request 1v or 2v it works perfectly, however it cannot go any higher than this. If I change easypdkprogtest to 100.0, it remains at 3.46v/3.44v.
Visual check of the PCB with microscope looks OK from what I can see.
Any ideas of what I should be checking to resolve this? Thank you!