Solution
The reason for this error is that these VIs are meant to run on a real-time target and they are mass compiled on a desktop target. LabVIEW thinks that the FPGA VI is a Windows VI, and runs the Windows compile chain for the VI, which then fails and results in the "Bad VI" error
The workaround to this is to go into the mass compile menu from the LabVIEW title screen instead of from the project explorer window: