I found out that there is a huge problem with generating font files that include kerning pairs in Fontographer 5.0. As update 5.1 fixes this, downloading the newest update (5.2 currently) from FontLab's website should fix this for You. There is also a kind of experimental solution with instructions available on their forums that You can try if You want to avoid updating but I don't recommend it since it didn't really work for me.
Update - found another solution:
Export the metrics from Fontographer and generate the font,
open the generated font in e.g. FontLab Studio and
import the metrics,
generate from the second program.
Update 2 -
You can also send your fog and fea files to email@example.com and they'll fix it if you are unable to do it otherwise