Sound out of sync issues

Hi. I've been using dvd::rip for a while now and it works pretty good to
encode a single dvd at the time. The other day I noticed the debug output
console which displays, amonst other things, the transcode commands dvd::rip
executes in the background. I figured, if I place a couple of these
transcode commands in a shell script then I can encode a batch of stuff over
night. This worked perfect, however, the sound seems to be out of sync...

This is an example of the two-pass command that I'm using (or that dvd:rip
seems to create for me):

mkdir -m 0775 -p '/home/user/temp/dvdrip-data/SES1D1/tmp' && cd
/home/user/temp/dvdrip-data/SES1D1/tmp && mkdir -p
/home/user/temp/dvdrip-data/SES1D1/avi/003 && execflow -n 19 transcode -H 10
-a 0 -x vob,null -i \/home\/user\/temp\/dvdrip\-data\/SES1D1\/vob\/003\/ -w
1800,50 -b 256,0,2 -s 2.724 --a52_drc_off -I 3 -f 25.000 -Y 4,0,4,0 -Z
640x360 -R 1 -y xvid,null --psu_mode --nav_seek
/home/user/temp/dvdrip-data/SES1D1/tmp/SES1D1-003-nav.log --no_split  -o
/dev/null --print_status 25 && echo EXECFLOW_OK

mkdir -m 0775 -p '/home/user/temp/dvdrip-data/SES1D1/tmp' && cd
/home/user/temp/dvdrip-data/SES1D1/tmp && mkdir -p
/home/user/temp/dvdrip-data/SES1D1/avi/003 && execflow -n 19 transcode -H 10
-a 0 -x vob -i \/home\/user\/temp\/dvdrip\-data\/SES1D1\/vob\/003\/ -w
1800,50 -b 256,0,2 -s 2.724 --a52_drc_off -I 3 -f 25.000 -Y 4,0,4,0 -Z
640x360 -R 2 -y xvid -E 44100 --psu_mode --nav_seek
/home/user/temp/dvdrip-data/SES1D1/tmp/SES1D1-003-nav.log --no_split  -o
/home/user/temp/dvdrip-data/SES1D1/avi/003/SES1D1-003.avi --print_status 25
&& echo EXECFLOW_OK

When I encode from the GUI everything seems to work fine.

Any ideas or hints very much appreciated.

Cheers,
Luke