http://handbrake.fr/) to do all my encoding. I have not had trouble using Handbrake to encode HD quality video into mp4. As far as I know Handbrake handles AVCHD formatted video as well.
That's the extent of what I know. I have not done any video editing/converting on the PC side. I believe Handbrake is available in Mac OSX, Linux, AND Windows...maybe give that a try?