I had a similar problem that manifested itself in virtually
stopping all network traffic if there is any activity on
the dialup-masq server (Pentium 100, 24Mb and plenty other services running)
The reason was that any HD activity stopped interrupts and serial port stopped.
The solution was to unmask IRQ with hdparm:
"hdparm -u1 /dev/hda" or wherever your hard drive is.
Read hdparm manpage carefully - it warns about the use of -u with CMD640
and RZ1000 IDE controllers. Your 486 might have of those.
If you use floppy-based router, that should not be the problem though.

I also use irqtune, but that didn't give any significant performance advantages
and didn't cure the above mentioned problem.

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