Snes9x2005 Plus stutters every ~7 seconds, works fine on regular APU

When using Blargg’s APU the frame rate shows as 59.8/59.7 most of the time and never reaches 59.9 unless I turn off audio sync or enable mute. This creates a very noticeable judder with scrolling stuff.

I’ve been trying to find a solution but no luck, the fps isn’t reported differently when using the Plus core so it doesn’t seem to be related.

Any help is greatly appreciated.