When this happens is it due to Google's past data on other advertisers using the same keyword getting bad CTR's or what? Landing page quality is ok.
Historical CTR of a keyword in Adwords as a whole is a factor but I am not sure how much weight it carries in the QS calculation. You say "initial" and certainly it seems since the new QS system was introduced that campaigns do initially start as you describe but they appear to sort themselves out after a couple of days. As long as the keyword relevance is okay and your ads and landing page are optimized you should see QS improve and the CPC drop.
If the CTR is really high it means that you don't have a good advert which should contain your keyword, or your landing page is not good enough (even though it's say "OK").
QS does drop a bit at first, but not for long. A while back I asked my Google account manager for some specifics, I got the following in reply: - If you add another ad variation, the quality score of any existing ad variations will not be affected - If you chose the option to have your ads rotate evenly, it is possible that the new ad variation will have slightly lower quality score for a short period of time. The system will quickly recognize that it is part of existing campaign - There is no specific time frame for the ad to gain equivalent quality score, this really is dependent on all the elements that make up quality score. I would however estimate several days.