Hi!
If I use the VBR Streaming LC-ACC profile, sometimes I get random clicks in the resulting mp4. I get clicks using latest in_mp4 for Winamp and also decoding the mp4 back to wav from within Nero itself (that's why I assumed it must be the encoder's fault). I don't know if it's clipping realted, but other presets (like Internet LC-ACC or Transparent LC-ACC) have no problem with my sample. The strange thing is that using foobar and foo_mp4, I don't get any clicks.
The attached flac contains my sample (4 seconds). If you use the VBR Streaming LC-AAC profile, you'll hear a click within the first second from the left speaker and a click within the last second from the right speaker.