my board behaves quite differently depending on whether or not the AVRISP mkII is plugged in or not. Could you please point me to any schematics of its device front-end?
My board is USB powered with a 3.3V LDO feeding off VBUS. An atmega32 provides basic housekeeping and has nothing to do with the USB interface. The USB interface is handled by a specialized controller.
No part of the board (other than ISP) uses SPI. I forgot to put in series resistors between the ISP header and the MCU.
I'm under the impression the AVRISP mkII programming interface is powered by the device it is programming, not by a regulator draining from its USB cable. Is that right.