If you're confused about why your ArduPilot 2.2 isn't putting your EM406 into binary mode when you've got the setup jumper/bind plug on (symptom: the yellow LED doesn't blink a few times on start, the GPS LED stays on and the blue ArduPilot LED won't stop blinking), it's probably because you didn't tell the software that you're using the EM406.
In the original EasyStar.h file, this line was set to default to the uBlox module (2):
//1-7
#define GPS_PROTOCOL 2 //0 = NMEA, 1=SIRF, 2=uBlox, Choose protocol, uBlox only for PRO's please.
The manual says to change it for your GPS, but it's easy to miss. Given that the EM406 is the recommended GPS and we say uBlox is only for pros, this wasn't a good default. So I've changed it to default to EM406 (1), so the code on the Google Code repository now has the following line:
//1-7
#define GPS_PROTOCOL 1 //0 = NMEA, 1=SIRF, 2=uBlox, Choose protocol, uBlox only for PRO's please.
Hopefully, this will solve the problem for those of you who were confused, and avoid more confused people in the future.
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