Audio desync problem

[Touya]

Here's what I'm doing:

I ripped the opening theme using File mode in DVD Decryptor, and the episode using IFO mode. Then, I added the opening and the episode vob files on DGIndex (Video Field Operation - Honor Pulldown Flags; Audio Output Method - Demux all tracks). Then I did the usual with GordianKnot to find out the filesize and loaded the avs into vdubmod. After encoding and muxing the .ac3 file with the video, the episode came out desynced. Note, the opening theme does seem to be in sync... Anyone know what's wrong?

[CWR03]

Check the two files, which probably have differing delays. If the opening theme doesn't need exact audio alignment, you can try changing its delay value to match the episode's delay. To do this, just change the value as displayed in the filename.

[Touya]

Hmm, neither ac3 file has a delay value.
I just encoded the episode separately and the audio came out fine. I can't seem to point out the problem. >.<