While I can't speak specifically for the Saab, or this crew/situation, I thought I'd chime in on the discussion. GPWS systems, and now EGPWS (Enhanced GPWS) offer several modes of warning. The system is intended to warn the flight crew of a possibly hazardous flight path, or incorrect aircraft configuration.
I'll reference the DC-9, for that's the one I'm most current with, although systems I've seen on the DC-10 and 757 are similar in operation. The system will trip if:
- An excessive closure with terrain is detected.
- An excessive descent rate under an altitude of 2,500 above ground level (AGL). (Sidenote: In the Navy, flying over the water we had the "minute to live rule". Never, ever have a rate of descent that was a value greater than your altitude. i.e at 2,000 feet and descending your rate of descent should be less than 2k, at 1,000 feet less than 1k, etc.)
- Altitude loss after takeoff.
- Excessively low on glideslope.
- Not in landing configuration under 500 feet.

Additionally, EGPWS predicts the projected path of the aircraft based on current flight parameters and determines if an alert is warranted.

The bottom line on GPWS warnings is that you have to honor the alert. There is an exception, but in the case you described... instrument conditions descending into terrain...you must honor the alert and correct the problem. The exception (and this has happened to me), is when it is crystal clear and you are cruising at 31,000 feet and the thing trips. Every now and then the system burps and trips a false warning....but for the most part they are reliable and when you are in the goo, low to the ground, and near terrain....you have to honor it. Sounds like these guys did.
Not sure what the reason might have been on this particular flight. They might have had excessive descent rate trying to get onto the approach. You can also get leveled off for whatever reason, then try and "make a play" to get back down to your altitude. If you push it over at say 2,000 feet for just a moment and violate that excessive vertical rate you will trip it.
Not sure if this clears it up or not, but thought I'd chime in.