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The firmware lets you set the actual reference frequency of the crystal in your QCX to get a more accurate frequency readout. (It uses that value to calculate the correct settings of the frequency synthesizer.) You can find the correct setting?in one of a few ways. If you have one of the QRP Labs GPS modules, you can use it to automatically set the frequency. If you have a frequency counter, you can measure the output frequency of your QCX, calculate the error, and then adjust the reference frequency accordingly. If you have a calibrated signal generator with a precise output, you can zero beat it with your QCX, and again calculate the error and adjust. You can set it in increments of 1 Hz, which is 0.037 ppm, a negligible error. (At 10 MHz, that would be a maximum error of 0.37 Hz. There are very few ham applications that require higher frequency accuracy than that. And it's going to depend somewhat on temperature in any case, so even if you set it to maximum accuracy on the test bench it might be a bit farther off when you operate the radio.)

The procedure for setting the reference frequency is now in the QCX operating manual, which is separate from the QCX construction manual. it's on page 35 of the manual for firmware 1.07. The procedure for calibrating using the GPS module is on page 36.

If you have the TCXO, the reference frequency needs to be set for 25.000000 MHz. The TCXO is specified as being accurate within 0.5 ppm, which would be an error of 5 Hz at 10 MHz. You can use the calibration procedure to set it more accurately if you wish, but most operators will find it unnecessary. If you do it, set it to 25 MHz manually first and THEN run the GPS calibration.

Your reports from the RBN suggest that your QCX is about 50 ppm off from the default value. You didn't report whether your frequency is high or low. adjusting the reference frequency down 1.35 kHz (to 27.002650) if your frequency is high, or up 1.35 kHz (to 27.005350) if your frequency is low, should get you much closer. That amount of error is normal for inexpensive crystals; there is nothing wrong with your radio, and it's why the adjustment is there. A more tightly specified crystal might cost 10 times as much and require a price increase of the rig.

It's also possible that the frequency accuracy of the RBN is less than perfect. Using GPS calibration is the best way to get the rig calibrated accurately if you have the GPS receiver for the QCX.