I think you guys should know, that R8169 driver in Linux is badly flawed.
There are several problems with the driver that I am aware of.
Of course there could be other problems that I did not face due to broad variety of possible chip revisions etc.
1. The driver does not init the chip properly, specially after dual-boot into Windows (no link detected)
2. Driver is not able to detect gigabit connection and falls back to 100 Mb
3. For some weirdest reason actual xfer speed with Windows based hosts can be anywhere between 1 kB/s and 500 kB/s.
I struggled with the last one and found that sometimes initiating a xfer with another non-Windows host may temporarily bring Windows host’s xfer rate to around 10 MB/s, but not all the time.
I wrote to the driver authors and distro maintainers but they all gave me a runaround or did not respond at all.
So R8169 is a bastard child of Realtek when it comes to Linux and the best solution is to replace it with 3com, Intel or another well supported chip.