Don't know why you don't see the 1000MB option for those servers (any possibility that it is plugged into a switch port hard set at 100?), but I do know that when streaming data (as BackupExec does) unless the server NIC and switch Port totally agree, you are much better off hard setting things. If you have NICs and Switches from the same manufacture, Autonegitate may work OK, but differing mfgs often have slightly different interpretations of the specs. For normal network traffic, you never notice it, but as I said when streaming, it slaps you in the face
I got into a rather heated discussion with someone here on the forums several years ago, and he quoted all kinds of tech specs and RFPs at me, I invited him to come to my shop, watch backups under both settings and tell me that I was either a liar or imagining things, but he never took me up on it. (This was with Compaq NetFlex3 NICs connecting to a Bay Networks switch.)