I have this same problem, but no remedy.
Ok so i have unlocked my device, installed SDK and asus drivers(several times).
ADB commands work fine, but my computer will not recognize the tablet in fastboot. I go into fastboot, and the "download protocol" message appears. I plug it in and then windows gives a message about the not being able to recognize the device. It just shows up as "unknown device" in the manager. It will not respond to any fastboot commands. I cannot flash a recovery.
I have tried directing it to drivers, but nothing seems to work.
Someone please help me see what i am missing. I have been trying for hours
Also i am on JB latest firmware...