You should not be disabling Auto on your Gb interfaces.
The IETF standard says,
"All 1000BASE-T PHYs shall provide support for Auto-Negotiation
(Clause 28) and shall be capable of operating as MASTER or SLAVE.
Auto-Negotiation is performed as part of the initial set-up of the link, and
allows the PHYs at each end to advertise their capabilities (speed, PHY
type, half or full duplex) and to automatically select the operating mode
for communication on the link. Auto-negotiation signaling is used for the
following two primary purposes for 1000BASE-T:
a) To negotiate that the PHY is capable of supporting 1000BASE-T half
duplex or full duplex transmission.
b) To determine the MASTER-SLAVE relationship between the PHYs at
each end of the link. 1000BASE-T MASTER PHY is clocked from a local source.
The SLAVE PHY uses loop timing where the clock is recovered from the received data stream."
99.9% of duplex mismatches are caused by people disabling Auto.