I was able to bypass this error by setting GPS_AUTO_CONFIG = 0 (disabled). Then after powering up GPS_AUTO_CONFIG = 1 (enable). Obviously I don’t want to do this every time or disable the GPS pre-arm check. Any help is appreciated.
It could be that there is a communication issue with the 2nd GPS or perhaps some other configuration is incorrect. Can you post an onboard load (aka dataflash log)? Ideally provide a .bin file they are much smaller and hold the same information as the .log files.