I can't say that I understand exactly why this would happen, but what I can say is that dual core is a feature that can cause all kinds of strange issues. If single core runs the game fast enough for you, I would strongly recommend using single core.
One thing you could do is check the game properties (right-click on the game in Dolphin's game list, then press Properties) to check that you didn't set "Deterministic Dual Core" to "fake-completion". I don't think you have done that, but if you for whatever reason have done that, that could explain what's going on.
One thing you could do is check the game properties (right-click on the game in Dolphin's game list, then press Properties) to check that you didn't set "Deterministic Dual Core" to "fake-completion". I don't think you have done that, but if you for whatever reason have done that, that could explain what's going on.