Hello,
I was troubleshooting a friends PC because they had somehow lost the majority of their fonts. I looked in Control panel under Fonts, and only 10 remained out of about 145 previously. However, I could still see the fonts in the when using the CMD window using the ATTRIB command, so the physical files were still there.
I restored the ccleaner .reg backup file, and the fonts returned to normal after a reboot. It appears that some link to the fonts were broken by the regclean process. Though I cannot reproduce this issue on my machine, I thought it was worth reporting it. Oh, and I am sorry that I didn't think to keep the .reg file. I wish I had it to attach.
It happened on Windows 7 Home Premium 64. Hope this helps, somehow.
RM