Have you tried using the latest development revisions of Dolphin? As of this writing, the latest revision is 4.0-609 as of this writing. You can find it here: https://dolphin-emu.org/download/ (scroll down).
If that doesn't help, additional things you can try are 1) disabling dual-core or 2) right-click the game in Dolphin, go to Properties, and enabled Sync GPU thread. Either one will probably result in some sort of performance cost (either slowdowns or increased usage of hardware resources if your system can handle these settings).
If that doesn't help, additional things you can try are 1) disabling dual-core or 2) right-click the game in Dolphin, go to Properties, and enabled Sync GPU thread. Either one will probably result in some sort of performance cost (either slowdowns or increased usage of hardware resources if your system can handle these settings).