I'm having the same problem - H.264 export crashes around the 1:03 mark every time. DNxHD is fine.
Dragging comps to Adobe Media Encoder and trying to render from there doesn't work either.
My CS6 install [last week] is on a brand new Dell Precision T7600 dual eight core machine with Windows 7.
It's ridiculous to say that we shouldn't render H.264 out of After Effects. Sometimes I render 50+ TV ads at at time from composition templates for delivery to a multitude of media outlets - each with slightly different specs.
Even if AME was a workaround, dragging all these comps over would be a crippling waste of time.
This is an Adobe problem and we've all wasted too much time troubleshooting and talking about it. PLEASE FIX.
Thank you.