ok this is to hopefully help some people. if you encode your file with mencoder and it is out of sync than just do this to the same file.
mencoder -ovc copy -o testin.avi testout.avi -oac copy
for some reason the indexing gets messed so it needs 2 passes
also while encoding the first pass to be on the safe side do this
mencoder in.avi -o out.avi -oac mp3lame -lameopts cbr:br=128 -ovc xvid -xvidencopts nogmc:noqpel:max_bframes=1:bitrate=800:me_quality= 3 -ofps 23.976
i hope this helps somebody out there