Yeah, I notice the same thing sometimes. There are some popouts that work really well (Potato Cod in Imax: Under the Sea and Guns in RE: Afterlife), but there have been a number of popouts in other movies that my eyes don't resolve well (read: nauseating) and I miss the effect. I will definitely try the sync invert trick with my projector and see if that helps. The problem seems to happen only with very quick popout moments and when a snow effect, for example, is supposed to spill outside of the screen. Oh, another example that is supposed to be great but didn't really work for me is the vampire deaths in Fright Night.
Video: Optoma HD3300, Panamorph UH480, Darbee Darblet, Samsung BD D6700 Blu Ray player, DIY Seymour Centerstage XD 138" Curved Screen
LCR - Tannoy DC12i, Sides - Tannoy IW63, Rears - Tannoy Saturn DC6ti Bookshelf, Ceilings - Tannoy CMS 603DC (TF), Tannoy CMS 601DC (TR), 3 Micro Marty/1 Full Marty DIY subs
Amplification: Emotiva XPA-3, Emotiva XPA-2, Outlaw Audio 7700, 2x Inuke 6000DSP
Receiver: Anthem MRX 720