I've enabled some debugging options but so far nothing seems to hit.
What I've been able to conclude is that there still is SPI
communication, the macphy interrupt is still pulled low, and the cpu
does the ack so that it's reset to inactive.

Is it doing this in an endless cycle?

Probably the debug tools are not showing anything because it is not
looping in just one location. It is a complex loop, interrupts
triggering a thread which runs to completion etc. So it looks like
normal behaviour.

If it is an endless cycle, it sounds like an interrupt storm. Some
interrupt bit is not getting cleared, so it immediately fires again as
soon as interrupts are enabled.

Is this your dual device board? Do you have both devices on the same
SPI bus? Do they share interrupt lines?

	Andrew