I know this is an old thread, but since the problem just happened to me, I figure others might get here with a search.
It hit me, but I was not using DVD2One. I was using other reauthoring software, and it was with a Sony. And it did play fine on my PC and on other DVD players.
So the answer seems to be a bit of both. It's the way Sony handles some DVDs with problems.
I copied my DVD back to my hard drive, and opened it with IFOEdit. I clicked on Get VTS sectors. For each VTS_XXX_X.IFO, I clicked on VOB Extras, or Menus Extras for VIDEO_TS.IFO. Since I didn't really need to strip any VOBs, I just rechecked whatever boxes were unchecked when it prompted for each IFO. Make sure to give a different directory for the output when you do this.
After it was all done, I burned a new DVD, and it worked fine on the Sony.
This leads me to believe that something wasn't quite right on the DVD, but IFOEdit was able to correct it.