I've got an XP system with the NVidia 7800 Graphics card, and I am not able to duplicate this issue.
Using Nero 18.104.22.168.b, and Nero Recode version 22.214.171.124, I add 4 Video files, and begin transcoding them. I then drag the Recode window to the second monitor, and the process continues encoding. I then drag it back and forth 10 times, and still it continues encoding. I then drag it so that the Recode window is half in one window and half in another, and it still continues encoding without any errors or 'Reset' occuring. And the resulting four MPEG4 files play back fully without problems.
I would have to say there is something about your system that may be a factor, as I am not able to duplicate this.