There's an easier way...just use shnfix -o shn * on your wav files. That way it'll convert the wavs to shns and fix sector boundaries all at the same time.
Otherwise, here's Scott's way around it, cut and pasted from an old post:
================
you can edit it so it doesn't add the "-fixed"
download the latest shntool source code. open up the fix.c source file (it might be core-fix.c or somethign, i can check when at home).
put a "//" before the #DEFINE postfix line
then down lower, put a "//" on the 2 lines that add the "-" and "fixed". or i'll send you the binary
(if you're a computer geek already then maybe i should have just said comment out the lines that add the -fixed)
================