Message Tracking sees the message, but it was not delivered to the mailbox
If Message Tracking (MT) has a record of the messsage in question, Exchange has received it.  If it does not reach the mailbox, the message is typically:
-  stuck in a queue
-  stuck in a routing loop
-  segregated by anti-virus/anti-spam filtering
You can often gain insight as to what is happening by reading through the audit trail of the message in MT.
Search the local and inter-server queues on all your servers.  If found, try manually releasing it and see what happens.
Check the logs of any 3rd-party anti-virus and anti-spam software.