I've got a 3220 that's negotiating down to 100Mb on the onboard copper ports. Switch has a 1GbE transciever in it and is set to auto negotiate. Has anyone seen this before. It's only happening on one of the two nodes.
If you have the ability to test the system while not in production - try plugging the two ports into each other and see if they autonegotiate to 1G or 100M. That would test both of them simulatenously. Also try forcing the switch port to 1G and see if it works.