Apple HE-AAC is only available up to 80 kbps. Not more.I don´t know how qtaacenc has managed to get HE-AAC at 96 kbps.
Does this happen when using QuickTime directly?
Cron,Can you post the short piece of this file (up to 30 seconds)?Also you can remove --he:--cvbr 96 --samplerate keep --highest - %d HE-AAC is disabled for bitrates >80 kbps for a good reason. It is not beter than LC-AAC at those rates.P.S. Not sure if --samplerate keep is compatible with --he (HE-AAC)
Have you tried other decoders yet?