Same thing happened to me...don't know if it was OS 10.4.10, FontCard 1.5 or
Suitcase Fusion 12.1.4.
Called Extensis, the very nice tech said he didn't know if they tested FH MX
anymore. I have a lot of custom sets that I didn't want to have to rebuild. The
tech suggested to drag the sets one by one to the desktop, which will collect
the fonts into a Collected Fonts folder. Next, in Fusion create a new empty set
and call it something like "All Fonts". Then in the drop down menu select the
"Suitcase Fusion Fonts" and select all fonts and drag them into the new All
Fonts set. Drag that set to the desktop as well. Then you can reinstalled
Fusion 12.1.3. The tech then informed me to drag the sets one by one back into
Fusion. VERY IMPORTANT...either do the "All Fonts" set first or last.

I tried this and still opening my FH files they would "forget" some of the
fonts for text boxes. Interesting test...if I just moved something and saved
the file and reopened it, the file would remember a few more text boxes....It
took about 10 saves and opening to get back to my original file. Not a very
good solution.

So, I trashed all the fonts from Fusion once again and added the fonts from
their original font folder. That seems to have fixed my trouble. Hope it
helps...I am back to 10.4.9 / FontCard 1.4 / and Fusion 12.1.3. I will try some
more testing.

Dual 2ghz G5 / OS 10.4.9 (Mac)