trying to delete this post but i just cant
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Cool idea, and it looks nice!
Possibly manufacturing variations, and of course, the sensitivity of the eye varies greatly with color. One way to fix that is to vary the LED on times.
The second issue is that the remainder minute LEDs (+MINS in the image above) are only on when an LED from the first minute column is on.
Are you sure that the PCB wiring is correct?
Is there a clever way to tell if the code is successful or not?
Measure the average supply current, and the supply current while sleeping. Beware that there are counterfeit ATmegas that draw too much current during some sleep modes.
it looks like they are all on at once.
The capacity of the CR2016 is about 90 mAh, assuming an average current draw of 100 uA and peak current of 1 mA. Since the LEDs each draw around 1 mA, and the processor draws 5 mA or so, expect battery life to be just a couple of days in that mode of operation.