Run a boil test and see how far they are off from the temperature of boiling water. Write down the temps for Food and BBQ.
Switch the probes and write down those temps. You'll then figure out if it is the probe or the Food/BBQ algorithm that is off.
My Food/BBQ difference is 2F on my Maverick, with the Food lower by 2F, which is similar to yours. I contacted Maverick when mine was new and was told that a 2-4F difference between the probes or the boil test is within their acceptable parameters.
A 3F difference in the chamber temp is absolutely nothing to worry about. What is important is the difference between the boil test and the Food temp. For example, at sea level water boils at 212F. If your food probe reads 209F in a boiling water, just mentally add three degrees to whatever your food probe is telling you. If it reads 215F, subtract three degrees from your food probe reading.
The temperature of boiling water is impacted by altitude, about 1F per 500 feet of elevation (.9F actually). So your test elevation can impact your reading too.