You can't compare boot times after format, to boot times after a period of time using the OS.
When you using the OS, you getting more and more software installed every time.
These software's got (most of them) services, and other features that effect the boot time.
These software's can also be categorized as malicious - Malware / Trojans / Viruses They can effect boot times while you even didn't know they exist.
- Make sure to clean your computer from any malicious programs.
- Make sure you clean and defrag the registry and your HD once in a while.
- Make sure that you disabled any unnecessary services and software's.