I just had this same problem during transcoding in Encore where my video timeline suddenly “being trimmed down”.
Video Format: DV-Pal
Video Duration: 2hrs 13mins
DVD Capacity: 4.7Gb
Transcoding: Automatic
I had no problem encoding the first disc which the duration actually longer than this one (2hrs 17mins) and manage to burn on a 4.7Gb DVD. Tried playing it on a DVD player and had no problem.
Anyway, I will try to use your method (re-encode the video from Premiere) and keep you posted on the result.