Solution
The PXIe-7971 is hardware-driven. Therefore, if you open multiple instances to the FPGA, it’s essential to ensure that you close the references correctly. Otherwise, incorrect closure of a reference can lead to unexpected behavior.
Regarding the 7971, since it is hardware-driven, when you close the FPGA reference, make sure you don’t have “Close and Reset if Last Reference” selected on the Close node. Selecting this option would put the FPGA VI into a stopped state. To avoid this, select “Close” instead.