You might want to take a look at the INDEXING service. Indexing will hog up a lot of system resources. When INDEXING is turned on in the Services, the computer is busy finding out where all of your files are located and this takes up some CPU time. Normally, INDEXING takes place when the computer is not being used, but it can start up doing it when you boot into the desktop. If you are not doing a lot of file searching, and you don't mind a file taking longer to be located on your computer when you do a file search, you can turn INDEXING service off in the system Services.
Also, you might want to check and see if you have set your antivirus scanner and any other malware scanners and see if they are set to scan your computer right away as soon as you boot into the desktop.
You will have to check your OPTIONS in each software to see if you have it set to IMMEDIATE SCAN ON BOOTUP or something similar (start scan automatically when desktop starts, etc).
Check to make sure you do not have an automatic disk defrag being done on startup (some proprietary scanners can be set to always reside in the background and start a defrag when the system starts up).
Check to see if you have a disk cleanup that is cleaning the computer of garbage files on startup.
Most of the programs that do this kind of automatic startup are also located in the System Tray, so check those out first. Also, check out your START directory to see what is starting up with the computer.
Just because your current software does not detect malware, does not mean something is not there. You should be using a good antivirus program (only one! because two or more antivirus programs can conflict with each other), plus at least two or three OTHER antimalware programs (which do not contain virus scanning properties).
Thus, you might have Norton or McAfee antivirus, plus something like Spybot S&D, Adaware 2008, A2 Free, Superantispyware or any number of other utilities which all need to be used and run on your computer. There are just too many security threats for any one software to catch all of them.