I'm running SuSE 9.1 with 512Mb RAM on an Athlon 2500, the mobo is an Asus A7V600 which has a built-in LAN controller which is a 3Com 3C940.

The 2.6 kernel has built-in support for this Gigabit ethernet controller in the guise of module sk98lin, which is said to be as good as (or even better) than the 3Com driver.

However, the transfer rate between this and other machines running Windows (sorry! test machines only...) seem only modest via a 100Mbps switch (no, I'm not expecting Gigabit speeds!). On boot, the card is set to half-duplex and no flow control. I should be able to set it to full duplex and with flow control with:
ifconfig eth0 down
rmmod sk98lin
modprobe sk98lin AutoNeg_A=On DupCap_A=Both FlowCtrl_A=SymOrRem
ifconfig eth0 up
... but it doesn't work - I've also tried adding these options directly to modprobe.conf and via YaST (which adds the settings to /etc/sysconfig/hardware/hwcfg-bus-pci-0000:00:09.0) and rebooting.

The syslog still shows the card starting up with the same (default) settings:
Jan 30 01:16:19 gimli kernel: eth0: network connection down
Jan 30 01:16:21 gimli kernel: eth0: network connection up using port A
Jan 30 01:16:21 gimli kernel: speed: 100
Jan 30 01:16:21 gimli kernel: autonegotiation: yes
Jan 30 01:16:21 gimli kernel: duplex mode: half
Jan 30 01:16:21 gimli kernel: flowctrl: none
Jan 30 01:16:21 gimli kernel: irq moderation: disabled
Jan 30 01:16:21 gimli kernel: scatter-gather: enabled
Jan 30 01:16:30 gimli kernel: eth0: no IPv6 routers present

Any ideas, anyone? Is there a chance the controller has been "hard-wired" to these settings on the mobo?

Well, the other end of the connection must, of course, also support these modes?