GitHub uses the open-source Pygments (http://pygments.org/) to highlight source code. If you can find the code for whatever ASM highlighter Pygments uses, you could probably fix it yourself. Though I tried searching for it and didn't find it after a while, so it would take some tracking down.
https://github.com/ReturnInfinity/BareMetal-OS/blob/master/o...
The 64-bit register names are still not handled correctly. It does properly color the 8, 16, and 32-bit register names.