It was mentioned Tanas, but XPort moved on really quick to another emulator. Last Ninja (1/remix/2/3) was one of the games I tried it out on, all the games my end have that annoying stutter. I don't know what kind of setup you have, but if you have the sound coming out through an external amplifier it's a lot more easier to notice, also if you ever use a set of headphones it's unmissable.
I don't mean to bring it up and annoy you so you're consciously looking out for it & spoiling your enjoyment, so I'm sorry for that.