When using Pages, one of my fonts types lowercase b when return key is pressed. I have looked at other fonts I have created with the same version of fontographer but can't see any difference in the glyphs.
Pages is apparently a word processing program for the Macintosh which is also (that is, Pages is also so sold in addition to the Macintosh) sold by Apple.
Given the post by Tom Gewecke, posted while I was typing the above, finding your post confusing, I remember that TrueType fonts, at least, have slightly different formats for use on Windows and Macintosh systems. Saving as a Macintosh font, thus, might help matters - although as I remember, the wrong type of font just wouldn't load, rather than causing mysterious bugs.
Might be worth a try to clear the font caches. How to here:
http://www.extensis.com/support/knowledge-base/clearing-the-mac-os-x-fon...
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Another report of something similar:
https://discussions.apple.com/message/19413834#19413834