I'm really not sure what is causing this problem. The letter "A" in my Frutiger font is getting cut off in FCP and AE and Motion. It shows up fine in Linotype FontExplorer and Word. It is in PostScript format if that makes a difference.
I have often seen this problem with graphics that were submitted in .eps format and other Illustrator formats. It appears that when you save the file, the bounding box gets saved too close to the actual image and cuts a portion of the graphic off.
You might try (if you have Illustrator) putting crop marks on the file that are maybe a half inch or so wider than the graphic all around. Also try saving the file to a different format to see whether that solves the problem. I have mostly seen it happen when I opened an Illustrator file (.eps usually) in AE, or brought it into an AVID system.
Creative Director / Multimedia Specialist
B&S Exhibits and Multimedia
I ran into a similar problem and found a solution. It is a font conflict. Check Font Book to see if you have a duplicate version of the same font. In my case, I changed the typeface to another weight and the issue went away.