I remember the glitch too, but I think I would've noticed a missing scene and well I didn't.
You can check with the Transcript that can be found here:
http://www.gilmore-girls.net/episode...cripts/09.html
I think it's just something wrong with the internal clock (or whatever it's called) on the DVD.
I actually just tried it and if you fast-forward a bit over the 12:07 mark at the end of act two (after the lorelai/emily phonecall) you get to chapter three with the right time.