Hi.
Strangely enough I have this same problem.

I installed GWX over a clean install of SH3 patched to 1.4. No probs there.
But on the 2 occasions I have played SH3 with GWX a reboot happens. The first time after 1.5 ingame days and the second time after almost 3 ingame days.
Both reboots happened while I was admiring the scenery from the bridge of my boat. And that was in the middle of nowhere, so not in a busy harbour or something. There was not a soul (or dolphin for that matter) in sight.
I do admit that my PC just meets the minimum specs (concerning RAM, rest is more than adequate), but plain old SH3 (1.4b) and GW 1.1a never caused any problems. So I am indeed baffled too. Could this also be SF related as Gizzmoe pointed out.

I really am at a loss here. Normally I don't have problems getting my games to work, but this puzzles me. I'm considering buying some more RAM tomorrow, but I wonder if that will solve my problems.
I was really looking forward to play GWX, but I'm afraid I've got to put it on ice for now untill I (or someone else) figure out a solution (boohoohoo).