Which Kindle, which FW version, and in case you're using my fonthack for FW 2/3, which freetype engine?
(Wild guess: broken bounding box settings. Check the ascent/descent/bearings & co).
I dimly remember a similar issue a while back, so you may also find something interesting in this very subforum with a careful search
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I've never had any issues with Fontforge, FYI. (But then, running Linux, it's not like I had much choice ;D).