I'll add a bit more hoping that someone will jump in.
I noticed files that contain the exact versions of the tools and libraries used to generate the pre-compiled Leonardo bootloader found in the GitHub.
Builds against LUFA version 111009
make version 3.81
avrdude version 5.11
All AVR tools except avrdude were installed by CrossPack 20100115:
avr-gcc version 4.3.3 (GCC)
Thread model: single
Configured with: ../configure —prefix=/usr/local/CrossPack-AVR-20100115 —disable-dependency-tracking —disable-nls —disable-werror —target=avr —enable-languages=c,c++ —disable-nls —disable-libssp —with-dwarf2
avr-libc version 1.6.7
binutils version 2.19
Some of the versions I was using did not match so I made some changes to use every exact version. On Windows, this led to a problem with avr-gcc 4.3.3, which compiles the bootloader to 4104 bytes, which doesn't fit.
I update avr-gcc to the latest AVR Toolchain, which produces a bootloader that fits, but still show the same error: "The device cannot start (Code 10)", in my Device Manager.