Yes, I know this is three years on.

The original post says
Then we want to (LOAD) a default TMPGEnc Template. Choose (VideoCD NTSC.mcf), you can use PAL if you are not in the states. NEXT you will want to load the VCD source file...........
Then click on (FILE) (ADD CURRENT PROJECT TO BATCH LIST) (MPEG FILE), you will do this over and over until you have all of the VCD'S loaded into the batch process......
What is this "batch process" in TMPGE doing?
Does it just read an MPEG1 and write it back in the same format? Presumably this tidies up timing errors from edits? Is the video resampled -- i.e. is there any loss of quality? 45 minutes per file sounds like it's resampling.
I've found I can fix sync problems in VCD-> DVD by first running the file through MPEGVCR's GOP fixer. Also VCDGear has a "fix mpeg error" function that seems to improve files; both these only take a minute or so per file so can't be resampling.