As Paul stated, I don’t trust AE for compression as well. I render out lossless and then compress in other software. I work in short form (2:30 or less generally) and it depends on the footage and how they want to view it.
If stuff is going to FTP for viewing I use compressor and H.264 encode everything.
If stuff needs to be emailed I use visualhub and make .mp4’s.
My 2 cents