Hi Doc,
Although I am not experiencing those issues myself, I can guess which
process(es) are responsible for those notifications and the CPU usage. Do you
have KPackageKit, Apper or something similar installed? There are also a couple
of different packages for update notifications related to this. You may want to
`dpkg -l *update*` and `dpkg -l *noti*' (for notify, notification, notifier) to find
packages related to this. I remember removing one or two of those packages
a while back, that got installed with an update.
Personally, I do not have very good experiences with these notifiers/GUIs on top
of apt, but if you actually want to use them then it may be worth investigating
more what causes the problems. If not, I would advise simply removing the
packages and using apt or aptitude directly.
Hope it helps!