It's more then likely your soundcard/processor overloading. In FL Studio make sure you're using the "Creative ASIO" as your sound device. It'll help prevent sound from crapping out on you (overloading), but it'll still happen when you have loads upon loads of Plugins loaded in and all playing at once. The only real way to fix all that is to buy a good processor and sound card. I've got a 6 core 2.8 Ghz and I don't get the slightest jtter anymore in FL Studio. And of course my Creative X-fi Music sound card, which I'm still going to replace sometime. hahaha, anywho. Hope this long rant helps.
AtomicEntertainment
Try some headphones perhaps? I've found them quite nice for editing films, seeing as how I can listen as loud as I wish, and with a great deal of quality. And if you're working with crappy speakers, this seems like an even more vital thing to do.
MisterJayElectro (Updated )
I am too stupid to deserve a music program. Wow. Thanks for the tip, it works fine now.
SUPER LATE EDIT: It worked fine until I started stacking plugins.....