hello.  This sounds like an issue with interrupt handling.  
Specifically, it seems like
interrupts from the controller are not getting routed properly after a while.  
Also, another way to reboot without having to power cycle might be to have a 
root shell open
before the problem begins after a reboot.  Then, when the problem occurs, use 
the internal kill
command to kil init with signal 9.  This should cause the system to panic and 
reboot.   It
would be interesting to know whether things work again after this warm reboot 
or if you need to
power cycle things to get the interrupts going again.
Some further questions:

1.  Are the two controllers on the same PCI interrupt?

2.  I'm assuming this machine ran find under older versions of NetBSD?  If so, 
were those older
versions runing with MSI/MSIX interrupts or the older style of interupt?
If the older style, check to make sure your motherboard and BIOS  support 
MSI/MSIX interrupts.
If you were previously running with the old style interrupts, make sure yur 
motherboard and
BIOS support MSI/MSIX interrupts.  Yu may need a BIOS update to get this 
working, assuming
newer BIOS updates are available for your hardware.
I'll note that MSI/MSIX interupts weren't used on this driver until NetBSD-10, 
so if you've
been running release versions of NetBSD on this hardware, you've not been using 
MSI/MSIX
interrupts on the mfii cards until now.

        If no BIOS updates are available and this is the first version of 
NetBSD you've been using
with MSI/MSIX  interrupts, try disabling MSI/MSIX and seeing if that works 
better.

Hope that helps.
-thanks
-Brian

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