Ok, I rigged up my serial cable as illustrated in the attached picture. I no longer need batteries to power the gps unit and this setup works perfectly with my laptop. But it still won't work with gpsapp. And I tried switching pins 2 and 3 just in case, but I think I don't need to because of how I connect my laptop to the empeg.

So I think I got the hardware part of this problem solved and now it is some software problem. I'll try going through all the software suggestions in this thread again to see if it makes a difference.