jack stutters/xruns when using onboard alsa/ALC887 but not with external USB sound
I have a Gigabyte GA-MA74GMT-S2 motherboard with onboard ALC887 sound. When I select the analog ALC887 as jack's interface, the sound stutters every couple of seconds and there are plenty of xruns, no matter how large I set the frames/period or periods/buffer. When I set jack to use my external USB Yamaha Audiogram6, it works fine. If I set the system up to use Pulseaudio instead of jack, then sound works fine with the ALC887.
My processor is an AMD phenom x4 945, and I have 8GB ram. Video card is Geforce GTX550 Ti. I am wondering how to make the onboard sound work properly (for when I don't have the Yamaha plugged in).
Any suggestions? Could this be a hardware conflict or something? I really need to use jack as I need some of the filters etc that I can run in jackrack.