Yesterday was, Today is, but ahh Tomorrow...mystery, suspense and a promise of hope.
if you open your C drive, click on view along the top and then check the box marked 'Hidden'. This will reveal your hidden files and folders. Open the Users folder and navigate to your name, App Data and then local. Look for a file marked icon cache and delete it. Reboot and hopefully your icons should be back to normal. Remember to uncheck 'Hidden'.
Sounds like a couple of you have a conflict or lack of compatibility w/ FontAgent Pro. Any chance you can live w/out it? Does anything change if it is uninstalled?
I especially muse this since, the other suggestions did no good.
You might give Sys Restore a shot, too.
I checked the Fontagent Pro site (insider software) and no mention of Windows 8 can be found. Details on how it's compatible for Windows 7 are present so it might be worth trying to run the app in compatibility mode. Anyway here's the sites knowledge base:
Insider Software - Makers of FontAgent Pro, a Windows and Macintosh Font Manager
Indeed, many programs that mess with the fonts and display in Windows 7 do not yet work in Windows 8. This includes the great screen capture software, FRAPS, as well. It is up to the developers of the software to fix these issues as best they can. There appears to have been an impasse with FRAPS, although a bit off topic -- the last release was in August. So I suspect that they know there is a problem in Windows 8 by now, and are working to fix it. If there has been no update to your software in the weeks following the public release of Windows 8, you may want to look at this as a compatibility problem with third party software. In this case, the third party software may not be compatible with the operating system at this time.