My mistake I meant to say programming logic, which in this case is the power rails and anything connected to the JTAG scan chain.
What is connected to the molex3 TCK, TDI, TDO, TMS, and TRST? Do you have some special connector to a FlashPro programmer? Or do you have some custom way to program the device?
You also didn't follow the recommended connections shown in this diagram in the Microsemi documentation:
View attachment 106741
I notice you don't have the VPUMP isolated from the VJTAG and the VPUMP isn't connect to ground through a 0.33uF and 0.01uF. It's recommended that the VJTAG and VPUMP not share a supply rail.
Regards