quoted

What is the link partner? From the datasheet

MMD Address 1h, Register 5Ah – 1000BASE-T Link-Up Time Control

When the link partner is another KSZ9031 device, the 1000BASE-T
link-up time can be long. These three bits provide an optional setting
to reduce the 1000BASE-T link-up time.
100 = Default power-up setting
011 = Optional setting to reduce link-up time when the link partner is
a KSZ9031 device.

Might be worth setting it and see what happens.

Have you tried playing with the prefer master/prefer slave options? If
you have identical PHYs on each end, it could be they are generating the same

'random'

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number used to determine who should be master and who should be slave.
If they both pick the same number, they are supposed to pick a
different random number and try again. There have been some PHYs which
are broken in this respect. prefer master/prefer slave should
influence the random number, biasing it higher/lower.

auto-neg should typically take a little over 1 second. 5 seconds is
way too long, something is not correct. You might want to sniff the
fast link pulses, try to decode the values and see what is going on.

I would not be surprised if you find out this 5 second complete time
is somehow related to it not completing at all.

The link partner is a switch (KSZ9893R) so I am not sure setting the 5Ah register
to 011 would help.

I set the 5Ah register to 011 and that didn’t help. I also am consulting the vendor and the hardware team regarding why autonegotiation takes so long with the KSZ9031. Will report back when they get back to me.