You really can't compare one boot to another. In order to any sort of statistical analysis, you really need a minimum of 20-50 boots.
The fact is, this can be anything in the background from applications performing updates in the background, Windows doing file checking or simply and sometimes it can be something such as temperature making a difference on certain components.
The most common cause I found was down to the hard drive, on 30+ scans of standard commercial grade drives, doing back to back performance scans can show a 5-10% performance difference...
There are just so many reasons it could be and it is really hard to help you here.