Sion,
FWIW, fonts can hide in a number of places. I'm assuming that you've
already checked the Master and Reference pages using Art's suggestion.
One sly culprit is a table definition stored in the Tables Catalog.
For every cell in the header and first row, the font information is
also stored.
Another less obvious culprit is an empty graphic text string. If
you've selected the graphic text tool, click anywhere on the page and
change your mind, there still is a null entry that has formatting
information. You need to do a Select All on a page to see if there are
any mysterious selected boxes that need to be blown away.
To really make sure that you find the missing fonts listed in the
console, you need to search in a MIF version of the file.
Otherwise, changing the Preference settings for remembering missing
font names and going through a save and open cycle will wash these out
of the file. Just remember to reset the preference back the way it
was.