Likely not a sector boundary issue any more. Can you open the offending files in soundforge, etc. and see what you're hearing?
Sector boundaries will not show up as a problem in a wav editing program, as what you're hearing is the zeros padded onto the end of a track by the cd burning program. However, there's a way in which a disk with sector boundary errors can be extracted to wav files and the wav files themselves will have the noise/error from the sbe in the wav file itself.
Bottom line, I'd be willing to bet that if the flac frontend won't fix what appears to be a sbe, shntool won't either