User gets the activate email and it stays in the inbox.
That is the problem. It should not stay in the inbox. BES should immediately grab it once it arrives. Could be a permissions issue on that account.
Use the IEMSTest tool to verify that the BlackBerry Enterprise Server service account can access her mailbox: KB02091-How to use the IEMSTest.exe tool to verify that the BlackBerry Enterprise Server service account can access user mailboxes
If that doesn't help, see this KB for troubleshooting steps: KB13852-Identifying and troubleshooting issues with the enterprise activation process