If you can manage the switch, make sure that you have forced the ports
to 1gig, if you cannot manage the switch, I suggest you change back to
Auto negotiate as this is probably how the switch is setup. Something
to try might be setting flow control on the hosts to "desired" for
send/recieve.
I don't know what that stuff is you pasted into your post, it almost
looks like a sniffer trace, but not quite.

Some things of interest
are the brand of Gig nic you are using, the specs of the machine, the
kind of cabling being used, the brand and model of the switch you are
using...
Again, if you have a managed switch, check the port error counters....
===========================
I have 3 PCs connecting to a Gigabit switch and a Linksys Cable Router
to the Uplink port of the Gigabit Switch. Connections to the Internet
works fine.. but transferring files between one another from PC to PC
is slow... similar to what I had before on the 10/100 switch even
after setting each NIC [within the control panel] in win2k to 1000
instead of Auto Neg. Please advise. Here is info from Sisoftsandra
2004b4. Did I do anything wrong ? Copying a 200-400MB file takes about
1-2 mins.