Right on all accounts. 23.976, Square pixels (not 960×720). Comp matches footage. But it even looks like that in the footage viewer!
I believe the QT engine might be frazzled. In the info panel for different footage, under Millions of Colors, I’m getting things like “apch” for ProRes, “qelr” for animation codec, “912v” for uncompressed, and “62vd” for DVCPRO standard def. Whereas in CS3 it properly reports the codec.
Last time I updated my Kona 3 software I also loaded the AJA Mac Plugins for CS4. But that caused output problems so I uninstalled them. I’ll reinstall After Effects and see if that solves the problem.
Thanks for the help David!