Same thing. If I turn off system update in application manager it stops. But that is treating the symptom rather than the cause I think .
This all started when I tried to update the prl. The pop up wouldn't start and the phone wouldn't look for a prl update. Same with update profile. Went to sprint zone and it gave me a you need to activate message. Phone seemed to be working fine before that as I was talking and texting. So went to settings and activated. All seemed to go well but the prl still wouldn't update. So I said the heck with it and I did a factory reset. Prl updated after that but this system update thing started to happen. So... I dunno.
Even if you turn the auto update off, it will update profile and PRL every time you turn on your phone. It is supposed to do that (the software was designed that way).