Kara, you're a god.
I haven't found EXACTLY what's causing the problem yet, but I know the problem is that, for some reason, the SR won't identify Freespace2 as a target window for events.
The code looks the same between the working build and the broken build when I looked at the chunk that handles initilization of the SR engine, so it must be an anomaly on the user end of things, but what could cause the SR engine to fail like that is beyond me. The only thing I could think of is that the SR engine was being initilized before Freespace2 had wormed it's way into windows accepting it as a valid window (after all, when I get the error messages, there isn't actually a window yet.)
This is when I wish I knew more about how graphical C++ programing in Windows really worked. lol
Thanks again for all your help, Kara, it's been mightily appreciated. And now I can get the codebase and really pour over this! I might learn something! XD