I'll try to read between the lines here. You have a Linux PC with an application that wants to use a parallel port to control something that isn't a printer. Your parallel port works under Windws XP and some Windows application, so you know the hardware works.
I will hazard a guess that either the Linux driver for your parallel port doesn't allow you to do things with the port that isn't talking to a printer, or the software expects to be able to find a real honest-to-gosh PC architecture parallel port, and yours is of some other variety, like USB. Programs like that are never going to work with that kind of hardware. Its very possible that the hardware isn't even capable, no matter what driver software is crafted.