Wow. Okay, I figured it out, and the cause was pretty unexpected. It seems that DXtory, which is a video capture and encoding program, somehow throttles Dolphin. I expected some lag, but it's actually a hard limit of exactly 25FPS. I find that pretty bizarre. Anyway, closing DXtory fixes the issue, so I'm gonna have to find another way of recording this game. 
Original thread QFFR below. Sorry for the forum clutter, but hey, it might help someone in the future.

Original thread QFFR below. Sorry for the forum clutter, but hey, it might help someone in the future.
Quote:I've been playing Rune Factory Frontier on 3.0-717 for the past week. Performance has been perfect. 100% game speed. The only slowdown was in areas of heavy activity, but it was perfect otherwise.
Today, I stupidly tried unticking some of the options in the game's properties page, thinking I might be able to squeeze a tiny bit more performance out out the laggier areas of the game. Why did I do such a dumbass thing? Because I thought "Hey, if anything goes wrong, I can just put the settings back how they were, rofl rofl rofl."
Except, that didn't work this time.
These are the exact settings I unticked:
"Enable MMU"
"Enable "BAT"
"Enable Block Merging"
"Enable Bounding Box Calc"
"ZTP Hack"
I loaded the game, and Dolphin decided to throttle the game at exactly 83% (25FPS, 50VPS). It's perfectly capable of going higher, it just refuses to do so. So I quit the game, put the boxes back how they were (filled boxes), and loaded the game again... and Dolphin is still throttling it at 25FPS, 83% game speed.
I can only conclude that somewhere, somehow, an inter-dimensional warp has fucked up my setup.
Here is how it looked before I changed anything, and also how it looks right now:
I must stress this: I did not touch ANY of Dolphin's "actual" settings. Those tickboxes are literally the only things I changed.
For testing, I made a copy of my Dolphin folder and tried changing the Framelimit settings. Even with framelimit set to "OFF", it is still throttled to exactly 25FPS.
I even re-downloaded the same Dolphin build and installed it fresh, and it's still limited to 25FPS right out of the box. What the heck? What kind of voodoo magic did I pull in order to get this running at fullspeed before now? I just don't know.
Please help. Any advice would be very much appreciated!