Could this be due to an outdated version of u-boot? I haven't had a chance to get Fedora on my BBB yet, so I don't know what version of u-boot is used/recommended in the image but I recall hearing about this in the OpenBSD mailing list:
"The last version of u-boot includes some important changes for the users
of BBB. With this version, the BBB runs at 1Ghz (now is running at
550mhz) when the board is connected to the power connector. The code was
developed by various developers of TI, so it's safe."