OP, just to test the game, which I bought as Collector's Limited Edition at Fry's in tin box with art book and mini action figures, I reinstalled and started playing it. Fry's had a killer deal on this version for only $20 shortly after launch.
First off, with your retail copy I believe your issue is with not having patch 1.4 installed. It contained a few bug fixes, and the server files. These are no doubt to verify CD keys without having to access a server.
When I install mine I just put in the key listed on the back of the manual and after install, the update tab says it's the latest version.
I am playing it in 2560x1440 via VSR, and it looks amazing. However to do the file edit properly, you need to also change the value of "seta r_mode" to -1 (seta r_mode "-1").
Whenever you want to edit resolution or aspect ratios, I find WSGF is a much better source of info.
http://www.wsgf.org/dr/prey That said, TweakGuides is also good, just not as easy to follow. However even in that guide it clearly states the need for a -1 r_mode...
r_customHeight [pixels] - Sets a custom screen height in pixels.
The r_mode command must be set to -1 to allow this to work.
r_customWidth [pixels] - Sets a custom screen width in pixels.
The r_mode command must be set to -1 to allow this to work.
I'm glad I read this thread because I'm really enjoying this old gem again, even more now that I can play it in 1440p. As for the claim it was a "thorough flop, it rated an average of about 84% on PC, and according to their CEO at the time Scott Miller, went gold within the first two months of sales.
There's solid reasons for that too. It had very good graphics for it's time, and their implementation of navigating through the game world via anti gravity paths, portals, and cubes was very well done. I also thought the shuttle segment was pretty creative, especially the way they appear and disappear at the shuttle bays.
In fact if anything I find myself worrying I won't like the new game as much. The puzzles alone in the old one were not always easy to figure out, and the gravity switches could be used to aid combat as well. It's a game that keeps you on your toes. You have to train yourself to look everywhere for puzzling AND combat.