There is a know problem with AutoTune and they way MOTU processes "bounce-to-disk". Antares is working on a fix.

In the meantime, here's the workaround:

1. Set the original track (with Autotune insterted) output to a bus (say Bus 1)
2. Create a new track, and assign it's input to Bus1. Record that new track.... Autotunes effect will print to the new track.

***Antares also have a software update which has fixes for other conflicts with DP. It's Autotune v1.55, and it's available at antarestech.com
This has to do with how the bounce is processed. When bouncing occurs as a realtime process (like in ProTools), it works fine. Autotune has a problem with "batch processing" - which is what MOTU uses for bouncing