@vaishak14,
Are you using a mapped drive to transfer?
Are you uisng a DNS alias to connect?
How do you know your cables are good?
SMB? Are you using that protocol to transfer or ? Which means you need NetBIOS or Beui installed to get the transfer.
Both NICs are set to 100/full or Auto? Drop your 1000 to work on 100/full and that might fix the problem instead of putting all the work on the switch to go down to 100.
Double check your cables though as damaged cables can cause a big reduction in speed.