This seems unlikely, but is there a defconfig that gets copied over your modifications to the .config file as one of the first things that happens when you do a "make"?

I haven't done much development for the beaglebone, so I'm not exactly sure which defconfig would be used. Typically the defconfig files live in the arch/<machine> directory, and for most builds you need to explicitly build the defconfig target, but maybe the beagleboneblack does something different.