I recently had a problem when DVD WS re-encoded a compliant MPEG-2. (In this case I wanted the file to be re-encoded to a lower bitrate.) DWS screwed up the field order. Here is how a help guy from Ulead showed me to fix the problem:

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First set your explorer View options to see hidden/system files.

Next browse to C:\documents and settings\all users\application data\ulead systems\ulead dvd workshop\1.0 and load the file "dvdws.ini" into Notepad.

Next look for the [VIODRIVER] heading and add Advance=1 to it;

[VIODRIVER]
Advance=1

This activates the Advanced MPEG encoder options in Make Video\Customize...\Compression

At the Finish step, click the make disc button then select customize, at the compression tab, click the ADVANCE button, under the Basic settings, set the field to Lower field first.
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A simpler way to deal with it is just to make sure you don't need DWS to rencode