Bad GPS Health error message

Have a hexacopter that was flying fine with arducopter 3.6.6. Replaced the cracked top cover with a new one which also has the GPS attached. Unplugged the two cables. Replaced the new top cover and attached the GPS. Plugged in the GPS 6 pin and 12c 4 pin cables. Nothing else was changed.
After final assembly I get a constant “bad gps health” message after I get 15+ sats and/or HDOP reaches 1. Have tried reattaching the cables at both ends. Also have a replacement exact same GPS (cirocomm L Doby) and cable which also gave the same error?
Any suggestions as to what it could be if is not the cable connection. Nothing else was changed just unplugged gps and replugged?
Hexacopter bin file

I am I right in thinking that generally a bad gps health message means a connection-communication problem from the FC to the GPS? Just having trouble understanding what the cause is? Right now I have 20 sats and a GPS HDOP of .59 with the error message every 15 sec.

Did you figure this out?

When I upgraded the firmware recently I get constant “Bad GPS Health” and “GPS Glitch” alerts. They last for less than a second and the copter has all the same sats and HDOP as yourself. I am using the HERE Gps. Hmmmm

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Not 100% sure. The only thing I did was reconnect the GPS cable several times and deselected the 3rd compass. Was still getting the error. Left it on the bench for the last week but I just booted up the hexacopter now and everything runs fine - no error messages at all? In my case I am guessing a connection problem?