In case you didn’t know, MacPro’s with 10.4.10 are connecting at 10Mb speeds to 1000Mb switches and hubs… bummer 
So a kext is the culprit:
/System/Library/Extensions/IONetworkingFamily.kext/
Contents/PlugIns/AppleIntel8254XEthernet.kext
In 10.4.9 it’s version is 1.1.7a3, in 10.4.10 it is 1.1.8a2, in 10.4.11 it is 1.1.8a6
That doesn’t matter much really, but that’s the details.
So you gotta roll back the kext:
1. Get the 10.4.9 Intel Combo Updater
2. Get OpenUp or Pacifist
3. Open the DMG
4. Show contents on the PKG
5. Copy out the pax.gz file to the desktop
6. un-Gzip the pax, and open that up (with Pacifist or OpenUp)
7. Get the old IONetworkingFamily.kext
8. Copy it into your /System/Library/Extentions
Now, the ownership on the kext need to be changed to root:wheel or if you’re in Finder system:wheel
Also, you should either delete the kernel caches or:
sudo touch /System/Library/Extensions
this changes the date stamp on the directory and OS X will recreate the kernel caches…
And yes, the 10.4.11 seed update corrects this.
Bonus Log files: These have been “prettied up” for readability, but you’ll see, 10.4.10′s driver is just spitting out Zer0s so the network switch/hub has no choice but to say “O K… I ‘ l l s p e a k s l o w e r t h e n…”
10.4.9:
Auto-Neg Advertise Reg (04d) = 0xde1,
Link Partner Ability Reg (05d) = 0xc5e1,
Gig Advertise Reg (09d) = 0xe00,
Gig Link Partner Ability Reg (10d) = 0x7800
10.4.10:
Auto-Neg Advertise Reg (04d) = 0xde1,
Link Partner Ability Reg (05d) = 0x0,
Gig Advertise Reg (09d) = 0xe00,
Gig Link Partner Ability Reg (10d) = 0x0
10.4.11(seed, much prettier logging in this kext):
Auto-Negotiation Advertisement Register (04d) = 0xde1
Auto-Negotiation Link Partner Ability Register (05d) = 0xc5e1
Auto-Negotiation Gigabit Advertisement Register (09d) = 0xe00
Auto-Negotiation Gigabit Link Partner Ability Register (10d) = 0x7800
PHY Specific Status Register (17d) = 0xaf48
If this info from 10.4.11 is NDA well bite me, I think people should know it’ll be fixed in the future, right? 
I tried this fix, but it did not work for me.
Worse, I have now installed OX 10.5, and the bug is still there ! My Mac Pro cannot connect at Gigabit speed !!! When an older G5 does connect at Gigabit speed on the same network under 10.4.10.
How frustrating ! I wonder if Apple’s developers are even aware of the problem??
I noticed something was indeed going wrong with my network after 10.4.10
Didn’t try to know why, just set manually the network speed to gigabit full-duplex and got back to gigabit speed. So the automatic recognition of network speed is wrong but it is at desired speed when set manually.