OK, then, let's get this made clear.
If you attempt to autonegotiate at 100Mbps, you will almost certainly get a duplex mismatch. Any duplex mismatch can destroy well over 99% of your throughput, under load. Where one might expect to run a steady 5+MB/S, a duplex mismatch can result in less than 20KB/S. The connection can appear to be good, with nice short latency, good times on large-packet pings, etc., but when you start trying to stream, outgoing packets stomp incoming packets, and vice versa. A stomped ACK for a correctly-received packet still causes every packet it acked to be retransmitted.
Check your server, like this(substitute your own physical adapter name(s)):
bash-3.00$ entstat -d ent1|grep Media.Speed
Media Speed Selected: Auto negotiation
Media Speed Running: 1000 Mbps Full Duplex
bash-3.00$
If your "Media Speed Selected" is "Auto negotiation" and your "Media Speed Running" is not "1000 Mbps Full Duplex", you know you have a problem before you even talk to your network guy. AIX can do 1000 only autonegotiate and all 1000bT connections are always full duplex, but there truly is no protocol for autonegotiating duplex, so usually your switch will go half and your card will go full.
If your speed running is NOT 1000, have your network guy do the equivalent for the switch port(s) you're using. Have him hard-code that port for the highest full-duplex you can both do, and then you do the same for your NIC.
I had a NIM server set up once and it turned out the switch was hosed, and running half-duplex. It made me look really bad when I tried to do a NIM recovery in a crisis. As always, it took nearly an act of Congress to get the network guy to eventually look at that port and see that it was running half though configured full. No other ports were available for us, but I got reasonably good performance by setting my server to half, to match.
The reason BBB has asked twice and now I'm asking, is that your issue closely resembles this one. If you don't look where the problem is, you probably won't find the answer.
Don't be like the guy I saw searching around in the bottom of his boat. I asked him what he was looking for, and he said he dropped his keys over the side. I asked him why he was searching inside the boat instead of on the bottom of the lake, and he said he couldn't swim.
