Hmm, smelling like maybe incomplete reflow. I don't do 0.5mm BGA that often and I had a bad paste print so I added flux and reflowed with no paste.
Pressed a bit on the board and after a power cycle its working fine so maybe marginal solder joint? Will need to investigate.
Either way, the problem of "when FPGA is configred, front panel MCU goes unresponsive over JTAG" persists and will be... fun... to troubleshoot.