Recently I tried it with my devcart and the same thing happens. In case it was accessing mirrored ROM, I duplicated the 2MB ROM as a 4MB image and loaded that, but the bug persisted.
What's weird is that I've used the same ROM with Kega and have completed the game and there is no bug during that part. Any ideas? I was using the known-good dumps (tried both (J) [!] and (B))
I assume a real cartridge of the game works properly?

Edit:
Seems if you don't use slow-motion during the entire fight there is no corruption! Very odd.