What are you doing to use shntool? A lot of people have issues with it, but it's always because it's not setup properly.
Have you read through the shntool guides I have at
www.audiophilia.net?
Also, note that I have a standalone program that is going to act as a frontend and proper installer for shntool and related programs that I've coded, though it's a few weeks away from being a reasonably effective "beta" product. If you can't get shntool running, and can be patient while I put a few touches on this thing, you'll have a nice way to use shntool without needing command line at all.
Finally, the only two other ways I can think of correct SBEs are to combine the whole show into a single wav file and split it up with CDWav or to decode to wav and use FLAC Frontend (make sure you have the newest version) to compress back to FLAC using the "sector align" option.
If you need help checking your shntool setup after reading the pages I setup, feel free to PM me.
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