Have to run auto-negotiate between clients and switch - "old" switch works fine - "new" switch results in "port flapping"?

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http://serverfault.com – I need some help understanding a problem we're having at work: We run Altiris/Deployment Solution and have to use auto-negotiate between client systems and our switches (Altiris apparently requires this for imaging, PXE boot and other functions). We have several areas with old wiring (Cat 3 & Cat 5) that have old 10/100 Cisco switches in them - and we can set these systems up to "auto/auto" (auto-negotiate on both the NIC and the switch port), and everything has been working fine. But - our networking crew changed out a couple of old switches for 10/100/1000 Cisco switches, and now - th (HowTos)