I'm not sure the transcoders can handle converting a font file containing CFF when it has to generate non-CFF in the SWF.
In theory, a font file containing CFF just has the CFF data copied when storing CFF data in the SWF for TLF and FTE. So if there is a CFF font file that isn't working for TLF, that implies that the player can't handle the glyphs.
A font file containing TTF is transcoded to CFF when storing CFF data in the SWF for TLF and FTE. So if the problem fonts are TTF, there are two points of failure: the transcoder, and the player's ability to renderer the transcoded data.
Anyway, if you have eliminated Flex code from the equation, then you might want to file a bug against the player at bugbase.adobe.com
-Alex