What exactly are you trying to do, "shntool fix"? I think the reason it's failing is because usually shntool fix will by default take samples from the second file to pad the first, and THEN pad the second file with zeroes at the end. Since the first file doesn't need padding, that's why you're getting the error. I guess you could try padding the other way, but I'd just track with CD-Wave instead, drop a marker at the very end and just trash the last file.
--Dave