I ran into this same issue from last year since IDE 1.5.2.
http://forum.arduino.cc/index.php?topic=171000.0
It is still an issue with the current IDE 1.5.7. However, I have been successfully burning bootloader with the AVRISPmkII by using avrdude-6.1. It appears they have changed or fixed this back-to-back timing issue with the latest avrdude version.
Check out the Windows binary http://download.savannah.gnu.org/releases/avrdude/avrdude-6.1-mingw32.zip or source code http://download.savannah.gnu.org/releases/avrdude/avrdude-6.1.tar.gz.