that looks like interlacing (or...worst case scenario, interlacing and blending)
did you de-interlace your source?
did you resize it?
you may not be able to do anything about it this time around. The only thing I can think of doing is making a little avs script.
you'll need the TIVTC package
the only way I know how to take care of this while still having a chnace of preserving your sync is to use TFM(order=-1,mode=5,PP=7,field=-1,slow=2)
I assume that you know about and have AviSynth (2.5.5 or later)
if not, you'll want to read up on it in EADFAG
when you get it, put the files into avisynth's plugins directory (or you'll have to use loadPlugin("pathToPlugin.dll") to get it to work)
I'm not 100% sure if you need other plugins as well, but if you do, they're all free