1. Maybe you installed something that now decides it wants to "load on boot". Aspects of Java, LibreOffice, and all manner of otherwise legit programs certainly aren't viruses, but suppose you missed some little box during the install.
2. While you don't use that specifically, MS Security Essentials decides it wants to scan bunches of stuff on boot, so then it "fights" for the boot cpu processing power during boot up.
3. It takes time for my machine to re-link all the shortcuts, again chewing up cpu power.