I've noticed a pattern where Google lowers my quality score on my high-converting keywords where CTR is fine. I used Google's conversion tracking system, which means Google "knows" which of my keywords are converting. Do you think Google would intentionally increase my minimum bid on my good keywords to maximize their profits?
No, I mean I hope not. There may be another reason for this but it's hard to say without looking at the stats etc.
Google use Analytics to determine your traffic and page. If you're being slapped, your not rubbing Google's dick well enough.
Your conversion rate has no bearing on your Quality Score. If it did, everyone would put their conversion tracking on their landing page, and get 100%. Since conversions mean different things to different websites, it wouldn't make any sense for Google to use conversion rate for anything. Google confirm this here: http://adwords.google.com/support/bin/answer.py?hl=en-uk&answer=93147
google don't look at your conversion rate, it's only for user. They are $250 billion company so they will not misuse conversion information.