Malware sometimes likes to invade the startup folder and other locations on infected systems. Seems that these are the hardest things to find and get rid of when trying to clean up spyware/malware/ infections.
You can hide Microsoft-signed entries to eliminate the good items from the list of things that start up on your system.
The application also allows information to be compared between runs. You will need to save/export scans to compare the previous to the current, but selecting File | Save will create the file needed.
We love this tool.