I was hoping the 3.1 update would resolve this issue. On import to the PluralEyes 3 interface, the video bin remains blank, only showing a rejection symbol after bringing in native EX3 mp4 video clips from Premiere Pro 6. If I convert the same EX3 video to ProRes 422 then import it to PluralEyes 3, it displays just fine. Even with Calibrated MP4-EX installed on my system, which displays EX3 video in other applications, PluralEyes 3 cannot process Sony's flavor of mp4 video.
Here's the rub. PluralEyes 2 for Premiere Pro CAN handle native EX3 mp4 video without any problem. I get by just fine with version 2, but version 3 offers real power on multi-camera double system audio productions.
Unless I am missing something, I hope RedGiant comes up with a solution in the next update.