I have about 266 items in my fonts folder, after installing the STIX fonts. Some of the files are transparent - not sure what that means. It looks like a bunch of fonts were installed by mathematica and by enabling east-asian language support/input.
Again, installing the STIX fonts seems to have resolved the issue for me, as it did for Borg. I would guess along the lines of Borg's hypothesis that when mathjax can't find the font it's looking for it starts trying to look through all the others, and the number (and type?) of fonts it has to look through might account for part of the typical length of the time during which the system is frozen.
Does this resolve the issue for anyone else? Particularly the people who said they were seeing warnings/error messages just before the freeze?