Much needed, as you know. Great for you to work on this.

A couple initial thoughts:I'd suggest getting the len part out first, if that's easier - checking to see if there are SBEs is the big issue and lots more people will check if it's easy. If they know they're there, they are more likely to do something about it.

Also, I'd STRONGLY suggest enabling and encouraging the use of the fix preview option - make the preview option prominent. Preview has two huge advantages:
- it makes it less of a black box - you can see exactly what it's doing to the files, always essential for good seeding. Always good to avoid using anything that doesn't tell you what it's doing to your files.
- you can see whether it's sorting the files in the right order - running an SBE fix if the filenames don't sort in order is worse than doing nothing at all, as it will move the bits around the wrong way

BTW, if you haven't seen this etree thread on batch files for shntool and shorten, have a look. Some of the discussion there may be useful to give you ideas on what features are useful:
http://forums.etree.org/viewtopic.php?p=11134

Nice installer, by the way - great that is has customization of the files installed and the location, always much appreciated. If it's not too hard, you might want to let people know that the uninstaller doesn't uninstall the codecs from the Windows directory. I can see why you did that, but it might be worth mentioning.

FWIW, Monkey's already has a pretty nice Windows GUI, I'm not sure there's so much need for that. It's shntool and shorten that are the GUI orphans, really.

QuickPar has a nice whole file md5 checker.

As for old school - hey, I used to teach at the old school. And the "old school" approach sucks big time in real life, as you can see from all the shows with SBEs and/or no seek tables.