AFP painfully slow
Just a hunch but it's quick to test. Try doing this on both Macs:
sysctl net.inet.tcp.delayed_ack
...note what it reports. It'll be an integer, probably the value 2 or 3...then set it to zero:
sudo sysctl -w net.inet.tcp.delayed_ack=0
...then on the AFP client, unmount all AFP-mounted volumes and re-mount them so that you're establishing new TCP connections. Then try your file copy test again and see if the speed is significantly improved.
I've run into situations where Mac OS X's TCP Delayed Ack algorithm was less than optimal, so it may be good to do this test to quickly rule that out.
For a long time now, AFP works over TCP, and it no longer meddles with packet size; or any packets in fact.
Nevertheless, i had an absurd experience with 3Com switches some years ago. It worked perfectly with windows and linux machines, with any kind of traffic i put there; but anything that involved a mac was stupidly slow (like 100kbits/sec or so). I called customer service and sent them lots of traffic captures; but as soon as they saw any packet that ethereal labelled as Apple...whatever, they said "we don't support appletalk" and closed the case. I managed to change the switch 3 times; but there was no difference.
needless to say, that was the last 3Com product i ever bought or recommended. Now i use DLink and Dell switches. no issues with those.
Of course, it's not your case.