Game-specific settings causing lag (Zelda)

[Renegade]

Both Wind Waker and Twilight Princess experience random but frequent FPS drops, for example, when opening a chest in Wind Waker or when there are enemies on screen.
If I open the graphics settings during the game, this fixes the issue, but I'm told this erases the game-specific settings.
So far in WW I can play fine without game-specific settings, but in TP, the minimap doesn't work so it's basically a choice between that or lag.

I'm running all settings on default/auto with no AA or AF, using real LLE. D3D11

Any thoughts on this?


Specs:
Operating System: Windows x64
Processor/CPU: Intel i2600k
Video Card/GPU: Nvidia GTX 570
Memory/RAM: G-Skill/16 GB
Dolphin Revision Currently Using: 4.0.2 x64