Does grepping your kernel log for "NIC Link is" reveal an unusual number of entries?
I experienced odd behaviour when connecting to/through a FritzBox (using multiple devices over Ethernet) a while back. When devices connected to any port set to "Green Mode" the link would seem to drop frequently when idle. The link would come up again when traffic arrived at either end, but a bunch of security protocols timed-out in the process and some applications failed in strange ways.
Saturating the link would result in a transfer stall followed by the link going down and then coming back up in 100Mbps mode. Continued saturation would even cause it to go down and come back up at 10Mbps... but at that point data transfer stopped. Software resetting of the link failed to restore it to 1Gbps — it required the power cycling of either the FritzBox or the device.
For some utterly unfathomable reason, the link was least stable on Port 4. Port 3 was half as unstable. Port 2 was about 1/10th as unstable. Port 1 was completely stable. However, since all local traffic had to use at least two LAN ports I ended up with instability regardless of whether I was on the sending or receiving end.
Forcing all four LAN ports into "Power Mode" — regardless of whether they needed to be there or not — solved the problem.
