Some people have been having issues uploading to their ArduPilot while the GPS is connected. I did some investigating today to determine where the issue may be.
I did a quick simulation of the circuit that turns the GPS on and off. This is a rough approximation, using a 650 ohm resistor to approximate the load of the GPS.
The circuit:

Results - Voltage across the load as a function of the voltage applied to the base resistor:

The minimum output high voltage specified by the ATmega datasheet is 4.2 V. So, it seems like it some situations the transistor might not actually turn off the GPS. I measured my board and found the voltage at the base resistor to be about 4.33 V, and according to the above plot, this means that my GPS should turn off, which in fact it does.
Comments?