I just finished my migration from Exchange 2003 to 2010. I was able to cleanly uninstall 2003 and we happy I had no reported user issues. Then our patch weekend were we patch and reboot all of our servers came along. On Monday we started getting calls about emails not being delivered. After some time with Google I found 3 different post with people having the same issue and two of them contact Microsoft PSS.
The fix is to use ADSIedit and drill down to
CN=Servers,CN=First Administrative Group,CN=Administrative Groups,CN=First Organization,CN=Microsoft Exchange,CN=Services,CN=Configuration,DC=domain,DC=local
Make sure the Servers folder is empty then delete the server folder. One note that I didn’t see in the other post, if you had multiple 2003 admin groups you need to do this for each one.
Now email flows to our public folders again! I just wish I could find a way to use sharepoint to replace the public folders, but so far I can’t find a way to start emails in sharepoint in the same eml format they are stored in public folders