I'd say, first of all, remove the ipod from the equation and just do a file type conversion, using an offending flac file, saving to a location on your hard drive. (right click file, library tools > convert format...)
If that file displays the problem, then you're looking at a possible decoder problem, in which case, you should head on over to the "3rd party plugins and skins" forum, find the flac decoder release thread (it'll be on the first page) and report your problem there, and scthom will have a look-see for you when time allows him.
EDITwas over there just now, so grabbed you a
direct linkIf that file is fine, then it's possible you have a sync problem, and you should persue the matter further in this thread.
Bear in mind that jriver/media center do not officially support .flac, so, try transcoding from a supported lossless format, ape or wma lossless and include those results too.
-marko.