Josh Levine has a nice write-up about a software only workaround for the Beagle Bone Black PHY issue:
Sometimes the Ethernet port on a Beagle Bone Black does not work on power up. It takes either a physical reset button press or a power cycle to fix it. This problem affects all BBB’s and until now could only be solved with hardware hacks.
The final official word from TI on this problem:
“There is no solution for this on the BB Black“
Full details at josh.com.