In this quest at least, the Stomp Boots work very erratically. Also, they only seem to work if you jump from the ground.
If the info helps at all, Link's jump is caused by a script that modifies the "Link->Jump" variable.
Pl33z3 fix.
(816) Oops, the Stomp Boots broke again.
The Stomp Boots are one of those things that require a bit of tweaking. Thanks!