Just upgraded my Surface Pro to Windows 8.1 at the weekend and had problems with desktop version of IE.
The 8.1. upgrade updates IE to version 11 from version 10 and by default Enhanced Protected Mode is switched on – even if you had it off in IE10 (default for IE10 was off).
After upgrading when I first started IE I got messages about add-ons being incompatible with Enhanced Protected Mode and I couldn’t do anything, browse the web or get options up.
Managed to get into Internet Options via Control Panel and noticed in Manage Add-ons that various add-ons including Lastpass, Evernote and even MS add-ons were listed as incompatible.
MS confirmed that this is switched on by default in IE11 but that not all add-ons including their own will be compatible.
I uninstalled any addons programmes I knew about, reset the settings for IE, unticked Enhanced Protected Mode (Internet Options, Advanced tab, Security section). Everything was then ok so I re-installed my add-on programmes.
I did a bit of additional testing – latest version of Lastpass was ok with enhanced protected mode switched on but latest Evernote (V5.0.2) was not.
So looks like best thing to do for now is switch Enhanced Protected Mode option off.
My test version of BreakThePaywall for Windows 8 was listed as disabled in Enhanced Protected Mode – this was almost ready for release but looks like I will have to make it compatible with Enhanced Protected Mode first. (http://www.breakthepaywall.com). Will try and get this rolled out before they release IE11 on Windows 7 as well.