it sounds like your messing up the framerate conversion somewhere along the line.
ok. heres a quick run through.
open up the demuxed ac3 audio from the 24fps original in besweet. now change the framerate from 24fps to 25fps exactly as in the screencap below
now click on the AC3 & OGG tab in besweet ,marked with the arrow in the screencap below., and change the bitrate to 640
now export your AC3
next convert the AC3 from 25fps to 23.976fps using eac3to.
once that is finished import the demuxed video file and AC3 into TSMuxer. make sure you click on the video stream and change the framerate to 2400/1. now before you create the new blu-ray folders you want to create a sample to test for sync. click on the "split & cut" tab and tick enable cutting . input the start time to about 100m and end time to about 105min (you can change these to whatever you want but towards the end of the movie will give you a good idea of the sync)
now check your sample. if this is in sync then you are good to go. if possible check on the media player you will be watching it on instead of using a pc player because sometimes sync goes out in a software pc player even though there is no sync problems with the file.