Change your avs script:

Avisource(My.avi,false)
AssumeFPS(25)
...
your usual script

You must to change audio with Overall Track Adjustements (OTA) in besweet from 23976 to 25000.
Run besweet gui, select input (your extracted ac3), select output (your rate changed ac3), mark "big endian PCM", mark "downconvert sample rate", select mp2, mark "change frame rate from", write 23976 and 25000. Click in "2lame" button, mark "sample rate" and write correct source khz (if ac3 maybe 48, see in virtualdubmod, file, file information), mark "encoding mode" and select dual channel, mark "total bitrate" and write 160 (or what you want), mark "add error protection". In engine select toolame, but if resulting audio es jerky, change to mp2enc, click in "besweet" button, click in "ac3 to mp2" button.
With besweet, you can select your avi like source then is better to select mp2enc engine (IMHO).