I think the problem you are having is due to MS's transition to relational database friendly OS. The registry will be non-existent or minimal in future MS operating systems as a result of this transition. The configuration for the system directories is apparently one of the early parts affected.
If this is the case, I don't know how to fix it, but I know where you'll want to look. Your problem will have to do with setting the value of FOLDERID_Fonts (CSIDL_FONTS). I would venture to guess that this is set by some .msc configuration application, likely one in the system32\en-US\ folder.