Hmm, if that's the case, that may not be something we can help you with. Problems with libusb and libmtp should be taken up on a forum or IRC channel that has people skilled with those libraries.
Although I am curious: How did you build the bootloader? From the looks of your output, it looks like you just built the single-boot bootloader, and not a patched nk.bin from the Gigabeat Updater.