Metroid Prime 2 framerate stutter

[DoubleD]

I just noticed that the recent versions over the last few months have been causing the frame rate of Metroid Prime 2 (GC) to stutter badly. I'm getting between 45-55 fps in the landing site area. It started in version 4.0-6904, while in previous versions (4.0-6901 and earlier) I get 60 fps in that area. There's even a little stutter in the startup menu. There was no problem in the recent version 5-rc releases however. Also, the performance in Prime 1 has increased substantially with the recent versions. It's a shame that didn't carry over into Prime 2.

Can anybody else confirm this?