I've experienced this with native 7 and PT HD 10 native. if it's only one instance (or a few), try and keep the plug-in as an insert and working in real time. or you can create an audio track and bus the tuned track to it and print it that way.
I tried a few things, including nixing the handles, and the only thing that worked for me was to change the AudioSuite version of the plugin's source clock from "host" to "internal" and render from the top of the session, not region-by region. Annoying but still a lot faster than printing.