On one of my Win8.1 upgraded machines, IE11 doesn't seem to be remembering cookies or passwords. I've done two factor authentication to google every time I open an IE session despite telling it to save password and remember and automatically sign in. Have had similar problems with other sites. (E.g.,answers.microsoft.com puts up the agree to terms banner every time I navigate to it...) Security settings appear to be the same on the problem machine as on the two that are working fine.
Makes me crazy how many things are showing up on one machine or another after upgrading all three.