AVRs are programmed over SPI, which is a clocked serial protocol. Many programmers include an option to change the SPI clock speed, because the maximum speed that works is dependent on the speed that the target chip is running at (1/4 to 1/6 of the clock rate, if I'm reading the datasheet correctly.) If you're running the AVR with a 32kHz watch crystal to achieve extreme low power, then you can't program it with 2MHz SPI communications. This usually shows up in the initial programming of the fuses; a "virgin" 328 runs off the internal 8MHz oscillator, further divided to give a 1MHz CPU clock. Therefore, you can't program it with a 1MHz SPI signal. Once you've programmed the fuses to use a external 16MHz crystal (for example), you can save some programming time by increasing the SPI clock rate.