I am using the stand-alone Bootloader_1_2_0 with a custom MK22F25612 board.
I have programmed this to use the USB HID interface.
When starting a debug session, it stops at a breakpoint at main() prior to bootloader_init() as expected.
Giving the source debug area focus with the mouse or moving the mouse over the debug windows will cause the KDS title bar to display "not responding" and nothing will bring it out of that state except closing the KDS application. KDS application restarts, re-powering the target board or resetting the computer (Windows 8) do not help.