bexicon,
Did you try item 1) in 5) of the list? That implies moving all the fonts out, then see, then move half the fonts in again, or something similar, to find every substandard font that might hide somewhere.
The following is a general list of things you may try when the issue is not in a specific file (you may have tried/done some of them already); 1) and 2) are the easy ones for temporary strangenesses, and 3) and 4) are specifically aimed at possibly corrupt preferences); 5) is a list in itself, and 6) is the last resort.
If possible/applicable, you should save current artwork first, of course.
1) Close down Illy and open again;
2) Restart the computer (you may do that up to at least 5 times);
3) Close down Illy and press Ctrl+Alt+Shift/Cmd+Option+Shift during startup (easy but irreversible);
4) Move the folder (follow the link with that name) with Illy closed (more tedious but also more thorough and reversible);
5) Look through and try out the relevant among the Other options (follow the link with that name, Item 7) is a list of usual suspects among other applications that may disturb and confuse Illy, Item 15) applies to CC, CS6, and maybe CS5);
Even more seriously, you may:
6) Uninstall, run the Cleaner Tool (if you have CS3/CS4/CS5/CS6/CC), and reinstall.
