Programmes, ADDONS to browsers - have you left task manager open when shuting down - select applications, firstly, and see if anything is there before shutting down - close any open programmes firstly, if there arent any now in device manager select processes and see which are the last left viewable if thats possible after starting shut down. There are 2 start up folders - one, start - all programs - startup - note down whats there two, type msconfig.exe in search, and select the result - in the window select startup - note down whats there also, ok if you restart the computer and shut it down immediately and its not slow that means its none of these programms are the cause - you could probably just assume that in any case - next you need to try and eliminate the cause, this narrows it down theoretically - if you have multiple browsers just use one for a period and selective programmes this may take forever but worth trying as you might strike it lucky.
Another suggestion is to use MSE security as its good and its microsoft this would eliminate the antivirus programme as the culprit if you havet already got it - Virus, Spyware & Malware Protection | Microsoft Security Essentials
Hope this maybe of some help - If it were me, as I have time to burn, and nothing else worked, I would do system restore back to the day i installed the OS, ie the first restore point and take it from there checking each program i installed.
Just leave it if you can live with it is my best advice, and try MSE - your decision.