By default, ATI cards underscan (possibly to ensure that nothing important is missed off the screen during boot) and the driver expects the application to fix this after boot. This gets in the way of over/under 3D output since some pixels are being moved vertically by the underscanning. This makes the left and right viewpoints separated by a significant margin and makes OU 3D viewing by default impossible.
Disable this behaviour by default with:
aticonfig --set-pcs-val=MCIL,DigitalHDTVDefaultUnderscan,0