Yeah, it's really frustrating. No idea what's causing the frame differences when I line them up against each other, maybe the IVTC plugin I used removed or added certain frames, even if it is just one frame difference, it makes it impossible to use this median script to get any good results. I'll try to line them up before IVTC, I just hoped that I would be able to avoid IVTC'ing them again.
Thanks for the report, seems they did an unusal awful job with that transfer. I noticed the squeezed computer display on your Beta, why not squeeze the end titles as well... weird. Your Beta screenshots will serve me well.
EDIT: Damn, thank you Moth3r! You're my hero. :)