Oops, that's your mistake. You can't fix just the tracks that have errors. You have to fix the entire set of seamless files together because shntool moves track breaks back and forth.

You can only skip tracks that don't need fixing if and ONLY if they come before the first track that has an SBE. In this case, that means you can skip track01, but that's it. Notice that when you fixed them with TLH, EVERY track except for track01 ended up with '-fixed' appended to it. That's not just there for fun, it's there to tell you that that track was changed.