I'm not sure of this (even though I should be, I've uploaded hundreds of videos to yt); but it might be that only the channels with a certain amount of subscribers and viewtime that get the higher quality compressions in youtube's own conversion. If youtube can monetize their videos, they are more likely to want the videos to be shown at better quality.
A mistake I made in the beginning was to view my own videos right after I uploaded them. At that point the HD version of them hadn't finished processing though, and thus I was watching the SD version. Now I give it a minute (usually happens when I put tags on the video anyway) before I watch, and at least that problem is gone :)