Continuing the discussion from Copter-3.5.0-rc7 is now available for beta testing:
@Paul_Atkin @rmackay9 asked me to reply to this as a seperate topic, so that’s why this is a new topic 
Regarding the first vehicle, autoconfigure is being used to fix the fact that your GPS units don’t have the correct/required configuration saved on them. If you were to set the GPS_TYPE 2 and GPS_AUTO_CONFIG 1 then it would be behaving fine. If you wanted to just save the configuration on the GPS once it’s been setup you could just set GPS_SAVE_CFG 2 which would save the correct settings for you after it’s fully configured which would let you turn of AUTO_CONFIG. However AUTO_CONFIG doesn’t change settings on the GPS once it’s setup correctly unless an error is detected, so I would recommend leaving that enabled.
Regarding the second vehicle, it’s detecting it as a ublox GPS as there was a ublox message detected, however the GPS isn’t reporting the full message set required, and it isn’t being configured correctly/on time and the driver is falling back to auto detecting again. Being detected as NMEA indicates the GPS is configured to only emit NMEA, and not the ublox protocol. This is not the desired configuration at all. Have you ever had this vehicle work with older firmware?