First of all, the Transporter R1 is a dual side, single layer DVD, each side having the widescreen or fullscreen version, which means that it can be copied directly from DVD Decrypter in ISO mode.
Second, the problem of chapter skipping or freezing, to me happens to:
a. Some random Decrypter ISO burns (Dunno why...)
b. Defective discs. (Princos mostly, but also TraxData etc) Some discs may play ok from start to finish, but has trouble in chapter hopping.
In fact, my goofy way of checking whether the burning is good, is insert it in the standalone and chapter hop till the end.
Goofy, but works
Have you tried it before or after watching the movie? In some rare cases, "hot" cheap discs respond in a weird way
Try a DVD-RW test.
I have also read the problem happening when using cheap CD labels.
I'm almost 100% sure your problem is not DVD2ONE related
I did it a couple of days ago (WS side) and started watching it with the wife. I had to stop it. Too much man stuff she said. So we watched "maid in Manhattan" instead ...
But checked the disc and it plays ok :). Burned on TayioYuden at 2X, new 1.30 FW on a Pioneer 105.