The error you're seeing is roughly 0.3%. That's not far from the 0.2% error I measured on an Uno a little while ago:
If your custom board is using a crystal then it's likely to be much more accurate. My Freetronics "Eleven" (an Uno clone with a crystal in place of the Uno's resonator) is accurate to roughly 40ppm.
If you can tolerate a small amount of drift, then I'd recommend building a second copy of your custom board, or buying something like the Freetronics Eleven. If you need better precision and can put the microcontrollers close together on the same board then it's possible to run off a single crystal (beware, the second clock is not wired in the same way as the first).