Can you be a bit more specific about the setup details?
This is a bit of a long shot. But in your detailed report, I noticed this:
/proc/interrupts
CPU0
0: 159264 XT-PIC timer
1: 2 XT-PIC keyboard
2: 0 XT-PIC cascade
3: 14174 XT-PIC eth0
5: 0 XT-PIC eth2
8: 0 XT-PIC rtc
10: 5374 XT-PIC eth1
14: 796 XT-PIC ide0
NMI: 0
ERR: 0
Does this host have any serial ports? Or, perhaps, a "software" modem (sometimes called a Winmodem)? The second is more likely, since nothing relevant shows up in /proc/ioports, and a serial port with a UART normally would. If so, you may be running into an IRQ problem on interrupt 3, the one you have eth0 using. (I've seen this before, but not for a long time.)
Try moving the eth0 NIC to a different IRQ (maybe 7 or 11, or even 15 if you have IDE1 disabled). OR go into the BIOS and disable whatever might be using IRQ3 (normally the second serial port or the onboard modem). Don't rely on kernel ITQ sharing, especially not if it is a Winmodem.
The rest of your more detailed report did confirm that the problem was on eth0 (the part about scp transfers between the router itself and your "external" LAN). So that is the NIC to focus your attention on, whether my guess is right or wrong.
BTW, in my (admittedly old) experience, the Winmodem problem manifests itself in complete failure to receive packets, so the "ip -s link show" results do not show large numbers of bad packets because they never reach the IP stack to be counted. But you might see large number of retransmits recorded by the ftp server.
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