this might be a long shot, but the program could have created some kind of structure problem or shrink is just too out of date to work with remake's output files.

try running the files through VOBBlanker (no settings, just select input, select output then click process) or FixVTS or some program like that...

use the processed files then try to open them in shrink.

if this doesn't work then there is something wrong with the files themselves that can't be just patched up.

i'd make a short test disc if this doesn't work just to make sure yu're ding things correctly as opposed to doing it ALL over again and coming out with the same result.