Beaglebone black LEDS not flashing

I have built the 4.1.24-bone-rt-r21 kernel and loaded it onto an sd card which I am booting from on the beaglebone black. However, when it boots, the LEDs do not flash. Any ideas why this might be? The LEDS flash if I use the 3.8.13 kernel so it is not a hardware issue. I also don’t see any boot issues except for the crap about libphy not finding the mdio (which occurs no matter what kernel I use).

Plug in a usb-serial adapter and show us what's happening at bootup..