When I pop Dr. M's version in my computer and my standalone DVD player, it says the length is 02:01:10.
I actually tried to adjust your AC3 file to work with Dr. M's, but I didn't get very good results. Granted, I'm a noob. Using Sony Sound Forge, I changed the pitch by -69 cents, and this lengthened the clip to 02:01:03. I got -69 cents by taking the total time of the clip, multiplying it by 4.096%, and then adjusting the pitch until it was as close as possible to the total number. Things were close, but the sync was still off.
I've never seen your version, but Dr. M's has a THX intro. Does your AC3 file account for this intro?