Thanks for the reply. I've also seen that post, but it doesn't seem to help. We created a new account and ported over the existing campaigns and the new account doesn't seem to have the same trouble. The bids are exactly the same in the new one. Very odd. In Microsoft's defense, this adcenter / yahoo migration is probably the biggest systems integration project of the last ten years. There will surely be issues.
Our rep did say other accounts are experiencing the same issues, but its shocking to me how threads exist online about the issue.