Yes, I have done all that.
I currently have a 3dr GPS + compass module (purchased from 3dr awhile back).
Currently, only the Mag port on the 3DR gps+mag compass is plugged in which connects to the I2C port on the navio2.
The 6 pin connector on the GPS is not connected to anything. After hours of trawling around the forum I came across this post this arvo. According the post, it seems that you do need to connect the 6way connector also. I will need to test this tomorrow when I get into work.
In your setup do you have the 6 pin connector hooked up? I was under the impression the 4 pin mag connector had power going in also. There is a small red LED that lights up on the GPS module when the cable is plugged in.