Emulator

Forgot to remove 7, ignore it ;D

use 50hz instead, theres no reason to change it and doing so usually does cause frame divisor issues in the emulator.

That's not a fix, that's a bypass....

True, but its all you'll get for now most likely.

The emulator doesn't handle the difference between 50 and 60 switching too well in the limited testing i've performend.

What you end up doing is trying to force 60frames per second through 50hz timing.

Try to enable progressive scan in the graphic settings and see if something changes.

Nope.

Also the game plays at 60FPS when disabling Idle Skipping...
However it skips frames every ~5-10 Seconds...

I also seem to be having a similar issue with the PAL version of the game. I can start the game in 60hz mode and it will run at 60fps until you enter the pause menu, at which point it will drop to 50 fps and stay there until the game is reloaded. The issue seems to occur on both Dolphin 4.0-1054 and Dolphin 4.0.1.

This issue still exists as of 4.0-r6535.

Using JIT Dual Core or JITIL Dual Core and OpenGL, you can easily see this issue in action by setting a breakpoint in Core/HW/VI/VideoInterface.cpp: UpdateParameters(). After booting and selecting 60Hz Mode, the game will regularly call this function, usually, but not exclusively, on screen transitions or when opening the menu as far as I can tell -- just run around between the different Rogueport screens for a while and it'll happen every so often. For a while it'll just re-set the NTSC parameters (m_DisplayControlRegister.FMT == 0), but eventually it will set the PAL ones (m_DisplayControlRegister.FMT == 1), and from then on it'll never set the NTSC parameters again.

This issue does not appear to occur at all in JIT Single Core or JITIL Single Core. Neither of those appear to ever call UpdateParamters() again after the initial Nintendo/IntSys logos.

This issue might be related to shader compilation in some way, as it occurs noticeably more often if you delete the shader cache for the game. It reminds me of the Metroid Prime 2 black bar issue.

If you lack the European TTYD to debug this, you can still see the UpdateParameters() calls on the Japanese (and presumably US, although I don't have that to test) version of the game, though of course without the actual effect on the framerate and horizontal line count.

Setting GPUDeterminismMode to fake-completion seems to fix this as well, so whatever the actual cause is most likely related to CPU<->GPU syncing.