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It is an OBOGS (OnBoard Oxygen Generating System) issue. I have only flown one OBOGS jets and that was only briefly, but it was still a pain. If anything hiccuped in the system it would shutdown. Most fighters don't maintain a tolerable cabin pressure above 28,000 feet so this can be a big issue.

I know several guys in two different types of aircraft that have almost been killed by OBOGS problems where the jet didn't even know it had a problem.

I also personally know a guy that died in an OBOGS aircraft where his last transmissions to ATC indicated that he was probably incoherent to the point of incapacitation. At the altitude he was at he would have had to have had his mask on, pointing to an OBOGS issue.

One in one hundred sorties is a fantastically high rate for such a critical safety of flight component. They really need to get this figured out soon.

A few years ago there was a Greek airliner (B-737) climbing out, when a warning horn went off passing about 10,000 feet.

The Captain assumed it was the takeoff warning horn (a malfunction) even though the oxygen masks deployed in the back as they climbed through about 14,000 feet.

The Captain went back to the circuit breaker panel while the first officer flew, and promptly passed out in the floor. The copilot continued the climb and eventually passed out at the controls.

The airplane flew for couple of more hours — eventually a flight attendant got in the cockpit (the intrusion resistant door was locked) who had some training in light aircraft.

The flight attendant couldn’t figure out how to operate the radios but flew it for a while until one engine flamed out due to fuel starvation and the airplane spiraled down into the ground.

Turns out the outflow valve was fully open the whole flight, preventing the airplane from pressurizing, because the Captain missed it on his cockpit setup.

Hypoxia is very serious and as you probably know any airplane with a cabin pressure above 10,000 feet must have supplemental oxygen. Most airliners cruise with a cabin altitude of around 8,000 feet.

But at 50,000 feet and up, where the Raptors like to be, the cabin pressure is likely to be closer to 25,000 feet, which is the altitude limit for unpressurized aircraft with supplemental oxygen. At those cabin altitudes hypoxia is more sudden and supplemental oxygen is a must under normal conditions, not to mention if there were a sudden loss of pressurization.

http://www.nytimes.com/2005/09/06/world/europe/06iht-crash.html