Hi, i am new to all this, but i had a similer oroblem just the other day. I took a 45min clip of an old movie, made a menu with 4 chapters (scene selection) saved it. then opened that encore program done what i had in there and thought just a matter of saving/ burning it.
When i trird to create the DVD or even to a dvd folder it was going to be 5.37GB I thought jayus. I thought i may have to to a dual later disc. Anyways i burnt / saved it to a folder and when i looked in the folder there was the VIDEO_TS folder at 1.69GB and also all the the other files too. it seemed to back up. saved all my original files too. hmmm.
I deleted those extra files and burned the video_ts file as normal … turned out great. try that it may help you.
Regards