TeaTimer doesn't monitor whole registry as that would.... do really big memory consumption and CPU usage. It only monitors registry keys which are mostly used by malware to execute it as soon as possible like Startup and Services entries, or to install some kind of stealth add-on on IE. Those entries which weren't monitored by TeaTimer are just entries like any kind of program would do, for example settings, saved data etc., and they aren't supposed to do actual damage unlike entries which TeaTimer blocked.

If TeaTimer was monitoring everything... It would keep asking you forever to decide an action for some entry from almost any program.