I'm having the same problem on a gigabyte board with built-in realtek nic. I've found numerous bugs for the same issue, not sure which is the main one and if ubuntu team is checking for duplicates. 

I have created a script on another machine that emails me when the link is down. I then crosschecked against all my logs and could not find anything related to the network going down.

This problem seems to be happening since 2.26.24 on r8169 (as per bugs I found).

My machine has two cards (second is a different brand), only the Realtek stops working.




==============================================================================

OS: Ubuntu Intrepid AMD64


Problem: 
Card stops working for a period of time (usually 5-15 minutes)

Bugs I found: 76489, 212497, 256331, 286489, 293661, 205374

=>lspci -vvv | less
03:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd. RTL8111/8168B PCI Express Gigabit Ethernet controller (rev 01)
        Subsystem: Giga-byte Technology Device e000
        Control: I/O+ Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx+
        Status: Cap+ 66MHz- UDF- FastB2B- ParErr- DEVSEL=fast >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
        Latency: 0, Cache Line Size: 32 bytes
        Interrupt: pin A routed to IRQ 2300
        Region 0: I/O ports at c000 [size=256]
        Region 2: Memory at f6000000 (64-bit, non-prefetchable) [size=4K]
        [virtual] Expansion ROM at fa100000 [disabled] [size=128K]
        Capabilities: <access denied>
        Kernel driver in use: r8169
        Kernel modules: r8169

=>cat /proc/version_signature
Ubuntu 2.6.27-7.16-server

=>ifconfig
RX bytes:10506838810 (10.5 GB)  TX bytes:1987163061 (1.9 GB)

=>dmesg
[169782.011271] ------------[ cut here ]------------
[169782.011278] WARNING: at /build/buildd/linux-2.6.27/net/sched/sch_generic.c:219 dev_watchdog+0x272/0x280()
[169782.011281] NETDEV WATCHDOG: eth0 (r8169): transmit timed out
[169782.011283] Modules linked in: vmnet vmci vmmon ipt_MASQUERADE iptable_nat nf_nat nf_conntrack_ipv4 xt_state nf_conntrack ipt_REJECT xt_tcpudp bridge stp kvm ppdev ipv6 iptable_filter ip_tables x_tables ac lp loop snd_hda_intel parport_pc snd_pcm snd_timer pcspkr snd evdev shpchp iTCO_wdt parport intel_agp button soundcore iTCO_vendor_support pci_hotplug snd_page_alloc ext3 jbd mbcache sr_mod cdrom ata_generic sd_mod crc_t10dif pata_jmicron sg ata_piix pata_acpi pata_it821x via_rhine mii libata r8169 scsi_mod dock ehci_hcd uhci_hcd usbcore raid10 raid456 async_xor async_memcpy async_tx xor raid1 raid0 multipath linear md_mod dm_mirror dm_log dm_snapshot dm_mod thermal processor fan fbcon tileblit font bitblit softcursor fuse [last unloaded: vmnet]
[169782.011353] Pid: 0, comm: swapper Not tainted 2.6.27-7-server #1
[169782.011355]
[169782.011356] Call Trace:
[169782.011358]  <IRQ>  [<ffffffff8024e91c>] warn_slowpath+0xbc/0xf0
[169782.011366]  [<ffffffff803a23ba>] ? __next_cpu+0x1a/0x30
[169782.011371]  [<ffffffff8024535c>] ? find_busiest_group+0x1dc/0x970
[169782.011375]  [<ffffffff80219d26>] ? read_tsc+0x16/0x40
[169782.011380]  [<ffffffff80273f44>] ? timer_stats_update_stats+0x24/0x370
[169782.011383]  [<ffffffff8026e491>] ? getnstimeofday+0x51/0xd0
[169782.011387]  [<ffffffff803a85fa>] ? strlcpy+0x4a/0x60
[169782.011390]  [<ffffffff80253e69>] ? set_normalized_timespec+0x9/0x90
[169782.011393]  [<ffffffff8047b452>] dev_watchdog+0x272/0x280
[169782.011396]  [<ffffffff8026ce9c>] ? sched_clock_cpu+0xcc/0x160
[169782.011399]  [<ffffffff80219d26>] ? read_tsc+0x16/0x40
[169782.011402]  [<ffffffff8047b1e0>] ? dev_watchdog+0x0/0x280
[169782.011406]  [<ffffffff80259f79>] run_timer_softirq+0x179/0x260
[169782.011409]  [<ffffffff80271704>] ? clockevents_program_event+0x54/0xa0
[169782.011413]  [<ffffffff80254d1c>] __do_softirq+0x8c/0x100
[169782.011417]  [<ffffffff8021417c>] call_softirq+0x1c/0x30
[169782.011420]  [<ffffffff80215875>] do_softirq+0x65/0xa0
[169782.011427]  [<ffffffff80254a85>] irq_exit+0x95/0xa0
[169782.011430]  [<ffffffff80226909>] smp_apic_timer_interrupt+0x89/0xc0
[169782.011432]  [<ffffffff80213983>] apic_timer_interrupt+0x83/0x90
[169782.011433]  <EOI>  [<ffffffff8021ab82>] ? mwait_idle+0x52/0x60
[169782.011437]  [<ffffffff8021ab39>] ? mwait_idle+0x9/0x60
[169782.011440]  [<ffffffff80210e95>] ? cpu_idle+0x75/0x110
[169782.011442]  [<ffffffff804fd205>] ? start_secondary+0x97/0xc2
[169782.011444]
[169782.011445] ---[ end trace aa5cac95cf032c52 ]---