AVRISP mk2 clone can program Arduino Uno, but not stand-alone ATMega328P
I had a similar experience before wherein I was using the AVRISP MK2 for a project. I was programming an Atmega32 with it and had shorted it by mistake. So initially, I tried burning a small code on the Arduino Uno with it and it worked quite well. But with the AVR it still wasn't working. So I borrowed a USBasp from a friend and tried burning the code on the AVR and it worked perfectly fine. So I wrote a mail to Atmel describing the problem and they had replied that there could be a chance that since the arduino IDE uses avrdude to burn the bootloader, it maybe using a different driver for the ISP. Anyways they suggested that the AVRISP MK2 may be malfunctioning and asked me to replace it.