Hello sgcole
I'm a little confused by this:
sgcoleCD-ROM drive is an eSATA ODD device attached to internal eSATA connection
I have checked the system board diagram and I cannot find an internal connector for external SATA(eSATA). Are you plugging this external ODD into the SATA_E connector? If so, that is not an external connector. That is one of the internal SATA connectors labeled SATA A/B/C/D/E. If you have plugged an external device to that connector then it could also be the cause of the USB connections not working. Check to see if USB is working with that device disconnected. Also, try the ODD in the eSATA connection at the rear of the server.
Thanks