New Nero AAC Encoder Glitch?

A month ago I updated my old Foobar2000 to version 0.92 which uses the new Nero AAC Encoder. At first, I really loved it. It allowed me to find the exact Q value that suits my needs instead of selecting from a list of presets like Nero AAC Codec 4.2.2.3. Songs encoded with this new Codec played great using Foobar, but once I put them in my iPod the honeymoon was over. Apparently there’s a glitch or some sort of incompatibility problem between this new Codec and iPod that results in the shortening the song by 3-5 seconds. That’s right. The same songs that played so well using Foobar are now 3-5 seconds shorter if I played them from my iPod. Has anyone noticed it?