I did the very same thing back in May and had the same issue. I think Windows 7 has a problem handling a certain amount of fonts so essentially its a matter of installing too many fonts for the OS. Back then I had installed a total of 58,000 fonts but I had to reinstall Windows 7 for another matter also. When I did that I was careful not to install too many fonts but 2 days ago I reinstalled with the full version of Windows 7 and I inadvertently installed too many fonts again. I'm not sure how because I was keeping a close eye on the number of fonts being installed and I was at 15,000 and somehow I jumped to 41,000. Apparently this issue doesn't just cause your fonts not to show in the fonts folder but also causes a lag in my system when booting up, opening programs and using some programs so its definitely a problem. I have started deleting some fonts throught the use of Windows XP Mode so hopefully I can get them down to a workable amount.