I cannot reproduce any performance problem at all on iPad 2 or iPad 3 with retina mode off, so this problem seems exclusively to do with iPad 3's retina display.
I am not sure why a certain window size would be considerably slower - I am fairly sure this is a WebKit/Safari bug, since we are running the exact same code either way - there's no reason our engine would be faster or slower either way. I would guess that certain window sizes either align or don't align with the main viewport, which enables or disables various optimisations (or even reverts to software rendering in some cases). Given that the iPad 3 is generally not fast enough to keep up with its significantly higher-resolution display, I would recommend just turning retina mode to 'iPhone only' or 'Never' for the time being.