We had a problem like this where the network switch and router didn’t auto negotiate at the correct speed.
The other thing to check is, if it’s an older building, the wiring in the walls. If it’s not wired to CAT5 standard it will work fine on the slower speed hubs but won’t auto-negotiate properly with the Gig switch. I have alot of customers that I have had to go back and repunch the ends of the cables installed to be CAT5 compliant. With 10M you don’t have to cross any wires and it will communicate at the proper speeds. At 100M if the wires aren’t crossed correctly it will work intermittently.
Also look at your nic settings on your SQL server and your workstation that are having the slowdown. See if their advanced settings any form of checksum offload or hardware offload and turn them all off.
Even thou you have checked for loopbacks between the switchs check again because this would be your number one thing that would cause this problem. Make sure that there is only one cable form this switch to any other switch.