I use Adobe Premiere Pro CS5.5 for encoding, which is also my editing software. If you too use Premiere then you will want to read my blog post on Max Render Quality in Adobe Premiere Pro and NVIDIA GPU acceleration.
It discusses the difference between software only and GPU acceleration, as well as checking and unchecking the Max Render Quality Box.
I also talk about frame rates as many of the presets have incorrect frame rates for your source material – don’t assume that presets are always the best settings for your footage.
