Can you check what is the QoS configuration on the PE connecting to Site 1 and Site 2. It may be possible that Site 2 might have some outbound qos policy configured.
Also, another quick way to test or isolate the SP network would be to attach a dummy CE at both site 1 and site 2 locations (locally in ur SP network not on the customer premises) and test teh file transfer.
Please share the configuration from both PE routers.
If this is Windows CIFS file transfer (??) be aware that there may be window size differences; particularly if you have windows server at one end and workstation at the other. This doesn't normally affect you much on a LAN, but on a WAN link, even if your FRAME size is standard ethernet, the window size for the file transfer may be different. Run wireshark during a transfer, and it may give you that information.
Another thing could be fragmentation. If somewhere along the path you have a lower MTU than the endpoints, packets may be split and causing additional delay.
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