As I said before it has nothing to do with the intrinsic speed of the program. It is exactly the same speed. The only change is the settings you are using.
Actually you are generally right but frankly 0.9.3 is *faster* than 0.9.2 using the *same settings*. So to properly compare you would use the Apple > Legacy > AppleTV Legacy preset in 0.9.3 (oops, just gave it away .. you can use 0.9.3 with the old 0.9.2 preset
among other things the x264 encoder is *much* faster in 0.9.3 with better output.