I had the same exact problem when I did this movie using DVD95Copy. The DVD structure and play was OK prior to transcoding but not OK after. I just thought it was DVD95Copy. Now I see that it also happens in DVD2one. After 3 tries of correct attempts, I still had the same problem but I had a workaround.
Though your DVD2One movie doesn't play properly, the final DVD size in your DVD2one will fit on a DVDR. You would have to replace each individual titleset VOBs in your original movie folder with your DVD2One and updating the original IFO using IFOupdate in "adjusted cell mode". If adjusted cell mode doesn't work, then use "cell mode only". Do this for all titlesets that got shrank. Eventually, you will get your DVD files in your original folder down to the size like your DVD2one's movie folder.
I'm not going in to details in on using IFOupdate as I don't have time and it's been discussed in this forum before. I played my new updated movie in my original movie folder in PowerDVD and IFOedit and it played flawlessly. It also played with no problems in my standalone after burning.
Hmmm...this is the first time I've experienced something like this. If it's a DVD copy-protection authoring technique, it's a good one.