I've never used microcontrollers before. I guess that brief activity on the pins when the chip is being programmed is normal? Is there anything that can be done to stop it effecting the circuit it is attached to? It doesn't effect my current project but might the next.
Upon power-up or reset condition the AVR chips default all their I/O pins to input pins with a high impedance (sometimes called tri-state) and any external components wired to the AVR I/O pins may be subject to a 'floating input condition', where just circuit noise causes false logic conditions. A typical 'fix' is to wire external pull-down resistors wired to the pin and ground, or pull-up resistors wired to the pin and +Vcc. This establishes a valid logic level if the AVR chip is powered off or in a reset condition.
Lefty