chances are it's either a background task, or more likely because you're using waitvsync to get rid of screen tearing which is generally a bad idea
waitvsync introduces lag, and also is going to cause hiccups when your screen refresh rate doesn't match the game refresh rate. by forcing away the screen tearing (a side effect of running at the wrong speed) you're just buffering up a tiny bit of incorrect timing over a period of time so that it never updates midscreen, but after a while you'll get a stutter when things jump back inline with the correct timing. waitvsync, triple buffer etc. are bandaids at best, with their own, often worse, side-effects.
the problem arises because most games don't run at 60hz, and until recently, most LCD monitors are fixed at a given frequency (often usually 60hz) with no fine control.
the only real way around this, without other side effects (eg games running at the incorrect speed or tearing) is to use a monitor that supports variable frequencies (so if you're talking LCD, one of the recent freesync/gsync ones) and turn off waitvsync.
one of the problems with a lot of modern emulation ports is they do change the games to 60hz to avoid this problem which causes them to run at the wrong speed and have sound/video desyncs etc. this appears to bug the hell out of people buying the collections to have an authentic experience, but really it isn't until more recently the tech to do it properly has been more readily available again. (CRTs could do this natively)