amateurasu wrote:They flicker even when I am using them, though. I was tinkering with the ATMega, wiring up all 12 LEDs from the ATMega pins to BUF1-12, leaving all the in/out jumpers disconnected, exactly as described in the user guide:
If you connect from the ATmega to the BUFx pins, then you're connecting the output to a buffer gate input which is connected to the LED. See the circuit diagram on page 12 of the manual. This is fine as long as you have both the input and output jumpers removed. In this case the output from the ATmega is not buffered, but it's driving an LED as well as what else you're connecting to it. ATmega pins can drive (IIRC) 40mA so you're OK with a bit more load directly on then than the Pi is.
If neither the input nor output jumpers are present, then this should be fine - the LED will reflect the state of the ATmegas pin - but if that pin is in input mode, then the LED will be indeterminate unless the internal pull-up on the ATmega is activated - at which point the LED will be ON. The LED will correctly reflect the state of the pin when it's turned to output mode.
Personally, I'd suggest connecting the ATmega to the Bx pins on the Gertboard, then enable either the input or output jumpers on the buffers depending on the pin mode on the ATmega - but you'll still get the same effect if the pin is set to an input (and the jumpers set to input) if nothing is connected to the BUFx pin.
"There is a third option for using this port: if neither the input nor output jumper is placed the I/O pin can be used as a simple ‘logic’ detector. The I/O pin can be connected to some other logic point (i.e. one that is either at 0V or 3.3V) and use the LED to check if the connect point is seen as high or low."
I still get random activity on the LEDs that aren't being driven at that particular moment, but which are still wired up and in theory being held low by the ATMega.
I'd double check your wiring and the jumper settings. Also study the circuit diagram - which I'll copy below:

"Raspi" is the Bx pin, and "I/O" is the BUFx pin on the Gertboard.
The only time the LEDs on my Gertboard flicker is when I've not connected anything to the buffers, or they're connected to the Pi and the Pi's pin is in input mode with the internal pull up/downs disabled.
-Gordon