U-Boot is the interface between X-loader and Kernel Image. Wrong u-Boot could disable your USB port and other things. If you want to use GPIO, you can also enable GPIO in u-Boot. The beagleboard x-loader looks for u-boot.bin file on your MMC card. If none was found, the beagleboard will use the default NAND u-boot.bin file, which could have the USB disabled.
Modify the file
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pico ./include/configs/omap3_beagle.h
make omap3_beagle_config
make
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