In an earlier post OXullo  indicated that the issue might be resolved with the latest kernel but I'm still seeing the issue with kernel 2.6.28-13-server #45 on a D945GCLF2 / Atom 330 mainboard. 

Testing with earlier kernals showed that putting a 100Mb/s switch in front of the server helped but did not resolve the issue.

kernel: [182129.000029] ------------[ cut here ]------------
 kernel: [182129.000038] WARNING: at /build/buildd/linux-2.6.28/net/sched/sch_generic.c:226 dev_watchdog+0x219/0x230()
 kernel: [182129.000044] NETDEV WATCHDOG: eth0 (r8169): transmit timed out
 kernel: [182129.000048] Modules linked in: video output input_polldev lp snd_hda_intel iTCO_wdt iTCO_vendor_support snd_pcm snd_timer ppdev psmouse snd intel_agp serio_raw soundcore pcspkr agpgart parport_pc parport snd_page_alloc r8169 mii fbcon tileblit font bitblit softcursor
 kernel: [182129.000096] Pid: 0, comm: swapper Not tainted 2.6.28-13-server #45-Ubuntu
 kernel: [182129.000101] Call Trace:
 kernel: [182129.000111]  [<c01411d0>] warn_slowpath+0x60/0x80
 kernel: [182129.000120]  [<c0133e6c>] ? enqueue_entity+0x13c/0x360
 kernel: [182129.000128]  [<c0139891>] ? enqueue_task_fair+0x31/0x70
 kernel: [182129.000134]  [<c012ff17>] ? enqueue_task+0x57/0x70
 kernel: [182129.000141]  [<c013b2cc>] ? try_to_wake_up+0xfc/0x280
 kernel: [182129.000149]  [<c02d39ad>] ? strlcpy+0x1d/0x60
 avahi-daemon[2709]: Invalid query packet.
 last message repeated 2 times
 kernel: [182129.000156]  [<c043b762>] ? netdev_drivername+0x32/0x40
 kernel: [182129.000163]  [<c044fdc9>] dev_watchdog+0x219/0x230
 kernel: [182129.000170]  [<c0153321>] ? __queue_work+0x31/0x40
 kernel: [182129.000178]  [<c014b6d0>] run_timer_softirq+0x130/0x200
 kernel: [182129.000184]  [<c044fbb0>] ? dev_watchdog+0x0/0x230
 kernel: [182129.000190]  [<c044fbb0>] ? dev_watchdog+0x0/0x230
 kernel: [182129.000198]  [<c01467d7>] __do_softirq+0x97/0x170
 kernel: [182129.000204]  [<c015a896>] ? hrtimer_interrupt+0x186/0x1b0
 kernel: [182129.000211]  [<c015a6e9>] ? ktime_get+0x19/0x40
 kernel: [182129.000217]  [<c014690d>] do_softirq+0x5d/0x60
 kernel: [182129.000224]  [<c0146a85>] irq_exit+0x55/0x90
 kernel: [182129.000230]  [<c011f8fb>] smp_apic_timer_interrupt+0x5b/0x90
 kernel: [182129.000238]  [<c010ac2c>] apic_timer_interrupt+0x28/0x30
 kernel: [182129.000245]  [<c0110a12>] ? mwait_idle+0x42/0x50
 kernel: [182129.000252]  [<c010884d>] cpu_idle+0x6d/0xd0
 kernel: [182129.000259]  [<c04f9fbe>] rest_init+0x4e/0x60
 kernel: [182129.000264] ---[ end trace 2a54a0b35234228f ]---
 kernel: [182129.041138] r8169: eth0: link up

Settings for eth0:
        Supported ports: [ TP MII ]
        Supported link modes:   10baseT/Half 10baseT/Full
                                100baseT/Half 100baseT/Full
                                1000baseT/Half 1000baseT/Full
        Supports auto-negotiation: Yes
        Advertised link modes:  10baseT/Half 10baseT/Full
                                100baseT/Half 100baseT/Full
                                1000baseT/Half 1000baseT/Full
        Advertised auto-negotiation: Yes
        Speed: 1000Mb/s
        Duplex: Full
        Port: MII
        PHYAD: 0
        Transceiver: internal
        Auto-negotiation: on
        Supports Wake-on: pumbg
        Wake-on: g
        Current message level: 0x00000033 (51)
        Link detected: yes