Check out http://www.doom9.org/index.html?/mpg/maestro2.htm
Use pulldown v0.99d or later (comes with DVD2SVCD 1.2.1 build 3) and run:
pulldown source.m2v target.m2v -drop_frame true
Create a NEW project with DVDMaestro (do NOT edit your old project) using the target.m2v file and add your subtitles, this should force the subtitles in sync.
Works for me, hope it does work for you too.