I have had an issue in the past with Womble MPEG Video Wizard re-encoding video when it shouldn't, and not notifying the user. You should still be able to tell based on CPU usage and how long it takes to create the DVD structure, if it's a long video.
They were very responsive to my query when I emailed them, and provided a fixed version shortly thereafter. I would suggest contacting them.
You might also want to upload sample before/after videos (MPEG files to a storage locker, not YouTube links) so we can see if there is any obvious reason that it is re-encoding the video. (You may also be able to tell from MediaInfo logs, for example if the GOPs are too long in the source.)
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