I've been running for about 3 weeks with a Realtek RTL-8169 PCI card
(turns out that the Intel card I mentioned earlier was PCI-e and I was
already using that slot) with no problems with large file transfers.

I also would like to mention that Ubuntu 9.04 with no kernel updates
will also display this problem, though much more infrequent than later
kernel versions. In other words, all kernel versions out there are
affected by this bug. Disabling the onboard LAN on the Shuttle and
adding an Ethernet card looks to be a workaround.

I found this in the 2.6.33-rc3 changelog:
(http://www.kernel.org/pub/linux/kernel/v2.6/testing/ChangeLog-2.6.33-rc3)

    net/via-rhine: Fix scheduling while atomic bugs
    
    There are BUGs "scheduling while atomic" triggered by the timer
    rhine_tx_timeout(). They are caused by calling napi_disable() (with
    msleep()). This patch fixes it by moving most of the timer content to
    the workqueue function (similarly to other drivers, like tg3), with
    spin_lock() changed to BH version.
    
    Additionally, there is spin_lock_irq() moved in rhine_close() to
    exclude napi_disable() etc., also tg3's way.

I hope this is related and gets merged into Ubuntu 10.4.

-- 
NETDEV WATCHDOG: eth0 (via-rhine): transmit queue 0 timed out
https://bugs.launchpad.net/bugs/454747
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