I've had a different Safari-not-loading-fonts-correctly problem for years. I posted a question about it 10 months ago, but there were never any replies:
https://forums.macrumors.com/threads/1266553/
Your problem is obviously a different one, especially as you're running Mountain Lion & Safari 6 as opposed to myself with Tiger & Safari 4, but the problems may not be entirely unrelated, as there may be bits of code in Safari 6 (or its WebKit) that haven't changed since Safari 4, and it may be down to one or more bugs in that code. Who knows? I've certainly not got a clue, but I thought I'd mention my problem here just in case it helps someone to solve your one.