I'm not aware of any speed negotiation problems with MSM APs. The AP ports are autonegotiating by default. If you force the speed on one side, the autonegotiating device can sniff the speed but not duplex setting. It will default to Half Duplex, and you'll end up with a Duplex Mismatch configuration.
So generally you should leave inter-device ports to Autoneg. This is also described in IEEE interpretation:
"This indicates that although operating speed is allowed to be manually selected by disabling Auto-Negotiation in Control Register 0, selecting 1000BASE-T mode of operation still requires that Auto-Negotiation be used."
http://standards.ieee.org/findstds/interps/IEEE802.3af-2003interp-6.pdf
Negotiation could fail for multiple reasons, including cabling / patch panels. So I'd suggest you get a brand new Cat6e cable for testing, take one of these APs and connect it directly to the switch bypassing all infrastructure cabling. If it works then you know where the culprit is.