have a look on this thread:
Basically, for now PC-BSD Update Manager doesn't work well with manual portupgrade, but the devs are working on solving this issue for 9.1.
You have all the details in the post to disable it from auto lauching, but you will lost all pcbsd update notification and will have to keep updated yourself further with portupgrade.
I still have to test all this by myself, as I'm really concerned with the 17(!) security issues that portaudit found on a fresh install of 9.0 with all patches proposed by the PC-BSD Update Manager
Hopes this helps...