There are a couple reasons for this. Here is a document that can explain some of those issues.
Also, we have ran into specific cases where a environment has a machine with a failed install/uninstall/upgrade. In this particular instance, this would usually leaves false registry keys. If this is the case you can check your ST.ServiceHost.Managed.Log for errors. This document explains this specifc issue further. http://community.shavlik.com/docs/DOC-23161
You will need to follow this guide to find about about logs and possible enable your logging to all/verbose.http://community.shavlik.com/docs/DOC-22921
As always, this information is for general purposes only and may or may not be your specific issue. If you would like specific help, I would suggest creating a support case at support.shavlik.com
I get the same on my end. Very annoying.