Not a Windows person, but ... the following is true of any platform ...
Are you attempting to upgrade from 2.6.x straight to 3.1.highest? Note the .highest there.
No can do. Must upgrade the 2.6.x to 2.7.highest first.
One of the changes for you is related to theme ... many themes, like the 'afterburner' theme you used in the 2.6 doesn't have a compat version in series 3.x.
Once you get the site upgraded to the 2.7.highest, check it for functionality ... especially any plugins ... get those upgraded and working as well.
Then *backup* the code + do a DB dump. Don't want to loose ground gained at the 2.7.highest stage.
Then try the upgrade to the 3.1.*highest*.
One cannot hyperjump upwards ... it's more a 'march'.
'spirit of sharing', Ken