Stupid question: is there any way to verify that in your case the supply voltage to the GPS is correct? Since the GPS is internal it may be tricky but not impossible. I'm not familiar with the schematics of the interface board (and in any case only own an APM1) but I wonder whether that could be the problem.
I have a similar situation with my current APM2.5 with MediaTek GPS.
It gets a 3Dfix in the APMPlanner when plugged into the USB. When outside, the GPS gets a solid blue light, but the APM board blue and red lights (A+C) flash about 20 times, then just the red light flashes. If I arm the board, only the red light goes solid.
I have also noticed that in the Mission Planner, even when there is a 3Dfix, there are no gps values on the status page.
I'm leaning towards a similar conclusion, viz. : there is a power problem between the APM board and the GPS module.
I don't have another GPS module or APM board to test with right now, but I have checked the voltage on the APM board and the GPS board: APM is 5.0v while the GPS module only gets 4.8v
I'm ready to order my next 2 APMs, but which GPS do I go for and which version of the APM? Is 2.0 more successful with the GPS?