I've posted this to another thread on this same subject, but in case you don't see it, here is a solution that worked for me:
1. I went through the Subsim.com link to Amazon.com and bought the pre-patched, no-DVD required version of SHIII for $9.95. I even got free shipping by signing up for a 30-day free trial of the Amazon priorty scheme (which I intend to cancel today). I did pay an extra $3.95 for next-day delivery, which happened as promised.
2. I had one small problem when installing from the new DVD - WIN 7 would not recognize the directory name I wanted to use: C:\Games\Ubisoft\Silent Hunter III\ giving me a message that the directory was invalid or unavailable because it was locked. After fighting that for an hour or so, I tried this one: "C:\Games\Silent_Hunter3\", and the load prceeded flawlessly!
3. After verifying the version was indeed 1.4 and that no DVD was required to actually start the Sim, I applied the GWX3 Gold mod, put the JSGME where it belonged, applied the .cfg changes to SH3 Commander, and (Hooray!), everything now works perfectly!
I must say my new machine is a killer (Falcon NW Mach V as of 1/2010). It allows me to run in compressed time mode at 4096 without a hitch, loads missions in seconds instead of minutes (a solid state hard drive doesn't hurt, nor does the I7 Extreme 95 Dual Core CPU), and I experience no delays while the harbor and surroundings load at the start of a mission. Searchlights at night no longer lock up the Sim or send me back to desktop.
The only thing missing are two mods I used to enjoy that I can no longer find anywhere - one applies colors to the ships on the map to distinguish friend from foe, and the other is an enhanced damage mod that creates large holes from torpedo impacts or gunnery hits. If anyone knows where to find them I'd be greatful!
Sorry about the bragging on the machine!

