Can you post a screen shot of the footage that is brought into Premiere before interpreting it, and after?
I have had the same problem. All i could do was select the first clip on the timeline, under modify click 'uniform scale', then control click the clip and selct copy. Then select the rest of the clips on the timeline and control click them and select 'past attributes'. Now all the clips are the right ratio.
Hope this helps you.
Is this on windows or Mac?
I have the same problem too-- but when I did clip/ modify / interpret footage / Use Pixel Aspect Ratio from File: HD Anamorphic 1080 (1.33), it still keeps video 2 at (1.0). Windows.
So, here's what I did that seems to fix everything. In the first example above, I hit "cancel" on the way in to creating the project in order to avoid picking a preset for the sequence. When I imported the footage, I created a sequence based on that footage.
However! When I found the preset based on my cameras output (AVCHD 1080i30 (60i) Anamorphic), I then created a new sequence with that preset, copied the media files to the timeline, hit save, export to FCP xml, and then ran Pluraleyes (v2), it worked perfectly. I'm guessing the problem is that PluralEyes is guessing wrong as to the pixel ratio for some reason.
Also, I believe I should be able to run PluralEyes from within Premiere Pro, but I don't see a menu item for it...anyone know about that off hand?