Unable to Receive Mail (Mail app)

I found the answer in our university's Knowledge Base:

Some Apple Mail (aka Mail or Mail.app) users running MacOS X 10.5 have been running into problems with the new mail.psu.edu AND email.psu.edu. To the end user, this issue manifests as Mail.app repeatedly prompting for the password and never successfully checking mail.

Here is what Mail.app is really doing:

Connects to mail.psu.edu OR email.psu.edu
Sends user ID and password
Fetches the list of all messages on the server (UIDL)
Disconnects
Compares the UIDL list to its internal list of messages already downloaded
Connects to mail.psu.edu OR email.psu.edu
Sends user ID and password

At this point, mail.psu.edu OR email.psu.edu returns the error "-ERR userID must wait n seconds before checking mail." Mail.app mishandles this and throws up the password prompt.

There are two issues:

1. Why does Mail.app drop the connection at step 4 then reconnect instead of maintaining the connection as it has done previously? AIT is working on this issue and has opened a bug report with Apple.
2. Why doesn't Mail.app handle the error message correctly? There is also a bug report opened with Apple on this one. (Note: this has been a running problem for Mail.app throughout its existence).

Fortunately, there is a workaround that will allow users to fetch their mail:

In Mail.app, go to Preferences➝Accounts.
Select the account.
Now select the Advanced tab.
Uncheck the box labeled "remove copy from server after retrieving a message."
Quit Mail.
Next, open the Finder.
Go to ~/Library/Mail (where ~ represents the user's home directory).
Locate the file MessageUidsAlreadyDownloaded3.
Delete the MessageUidsAlreadyDownloaded3 file. Note: If there are other files with similar names, delete those as well.
Using POPsickle at https://helpdesk.css.psu.edu/listpop/popsickle.html, delete all mail that has already been downloaded by Mail.app/seen by the user. IMPORTANT: This is critical, as the list of messages already downloaded was removed in step 9. Not completing this step will result in ALL mail being downloaded again.
Wait five (5) minutes.
Launch Mail.app and try again.

From this point forward, mail checks should work. However, all mail will be left on server. We recommend users plan to periodically purge accumulating mail with POPsickle until the problem is resolved.

This solved the problem for me. Mail is not checking mail normally. This problem may have arisen after I deleted about 100 emails in my inbox. Hope this helps someone.