So I finally figured it out....as soon as I disabled weather updates, the behavior stopped, must have been something to do with the wind changing? My refresh rate was set to 120 minutes so I'm not sure why it would do this, maybe a bug. At least I finally found the problem, I was pulling my hair out.
Whenever I get to cruise altitude, the autothrottle makes really drastic adjustments to maintain speed, the epr will jump back and forth between 1.0 and 1.5, very rapidly every second, to the point where you can hear the engines spooling up and down dramatically. I tried setting different speeds, from .82 to .86, even tried different altitudes, but it keeps happening. Is this a bug in the plane, or am I not setting things correctly in the FMC or elsewhere?