Newer revisions past 4.0 409 causes Resident Evil 4 to freeze in the fly cave.

[Shonumi]

You should pinpoint the exact revision that introduced the issue and report it on Dolphin's Google Code page. It's the best way to bring up a problem to the attention of the devs, thus making it more likely to be fixed. Believe it or not, but a number of devs don't like using the forum (and not just as it pertains to fixing Dolphin related issues) so be sure to let them know on the project's page.