Problem is actually even more complex when you deal with links coming to your site from IE8 emulation BLACKLIST sites such as Facebook.
A shared link on Facebook causes your links to open in a Popup - IF THE "INCLUDE UPDATE WEBLISTS" is checked on the compatibility view settings, which is checked by default, the popup window sees the Blacklist referrer from Facebook and opens the window in Blacklist mode initially. When detecting in background for Trident\4.0 - you will see the value, and set the downlevel CSS.
However, after the browser loads it switches out of Compat mode and changes to STANDARD mode without refreshing. You therefore have the wrong CSS for standard modes assigned.
Solution - Force the IE Browser out of Compatibility mode. Yep - seems odd, why let a user go downlevel on your site if you don't need to.
Just like Downlevel you set IE=EmulateI7 to force the browser down you can add IE=EmulateIE8 and force the user to view your page in IE8 Standard. this mode even removes their ability to select Compatibility View and reduce your Test Needs for that mode