Hi guys,
We are aware of this and are working on a solution. Right now transfers through fpga are a bit slow. There are two solutions:one is using fpga in bypass that basically connects Sam pins directly to Nina and requires Sam peripherals so wastes some mkr pins. The other is an optimization we're doing on the JTAG interface. The latter should come in a few days. The first is immediately available although not documented. Bottom line... Please wait a few days and it should improve significantly.