you will right if the problem is (or was) the mpeg2dec3!
i'm using the same mpeg2dec3_25_dll_20030728 like you
and don't have problems...Kwag is using too, and this is the last version!
i can be wrong but i think that mpeg2dec.dll (if i remember)
for avisynth 2.5x, can be used only with dvd2avi176 !
but like i posted (there), i think that CQ58.1 too low
for 101 minutes using 544x480.
try to use 480x480 to encrease the CQ and
use 2500 for maximum bitrate in Tmpgenc!
after find the new CQ, encode a sample using trim on the script
using the same scene where you got problems and compare!