This is a known problem that the Nero team is hopefully working on solving for the next version. See the following thread:
http://www.hydrogenaudio.org/forums/index....showtopic=57805Even if you use the low complexity profile, which, as lvqcl pointed out is required, the files will not copy to an iPod Shuffle 2nd Generation. The current work around is to use the "Optimize MP4 Layout" feature of foobar2000 (found in the Utilities contextual menu).
The latest, albeit incomplete, listening test by guruboolez (found
here) indicated that the latest version of the Nero Encoder may producer lower quality files than the February 2007 build, at least when encoding classical music. You may want to try using the older build until Nero has resolved these issues, or simply use iTunes to encode using iTunesEncode46 to access it via a CLI.