I'm using Premiere CS6 and PluralEyes 3 and I can confirm that this issue is still present - I started my workflow in Premiere, importing all media into a timeline, and using the extension to bring the project into PE3. I exported a synced (but not replaced) timeline out of PE3 and brought it into Premiere.
I edited the project and didn't add a dynamics filter until the very end. After a save, close and reopen, the error comes up that the filters are unavailable, and in the effects panel they are offline.
Sucks.