I'm having a similar problem with the homebrewn EPROM emulator (designed by Jeff Frohwein) that I'm using as my NES devkit. The dumping program works fine in pure DOS mode, dumping the ROM, resetting the NES and then giving you back a DOS prompt allowing you to do other things while the NES ROM is running. In Windows however, all my attempts to use it have failed, since Windows seems to play with the parallel port at random occasions, making the EPROM emulator whack out during download.
I've tried several different methods, both using two different hack programs called porttalk and userport that allow DOS programs to write ports normally, as well as using the "right" way by using a win32 library called WinIO to write the port, but the only thing that will stop windows from randomly(?) interferring with the LPT port is disabling the device in the device manager, but then none of the abovementioned products have any effect. I haven't tried it at all in Linux since I'm a Linux newbie and wouldn't even know where to start.
Having to use my old broken P100 laptop for all NES development sucks badly, so if anyone knows how to solve this problem it would be greatly appreciated. :)
(The original source code for the device can be found on http://www.devrs.com/e/files/ee.zip)