You can give this a shot:

Settings>Applications>Manage Applications>Dialer
Settings>Applications>Manage Applications>Contacts Storage

 

I use the stock HTC dialer.

 

I had the same problem after I did the OTA upgrade. After reading a lot of the forums about the factory reset, I joined in.
That fixed the speed dial issue and a few others I noticed.

 

If you did the OTA 2.1 update, you probably need to do a Factory Reset like
jrobinson317 said. Look at: http://androidforums.com/htc-droid-eris/80233-factory-data-reset-option.html

http://androidforums.com/htc-droid-eris/80672-speed-dialer-issues.html

 

I agree, and I normally will suggest a factory reset, I had just come across this post, and though it was worth a try if the person didn't want to hard reset.

 

This absolutely works. Thanks for the solution, this was driving me crazy. You just need to re-sync your contacts afterwards, assuming all of your contacts are saved on Google, which thankfully mine are.