How long has your pH probe been in the water? I'd give it at least a week before calibrating.
I also don't recommend using the automatic calibration procedure.
Go to Advanced and then hit manual calibration.
Make sure your pH solutions are at aquarium temperature. I put mine in a water bath in the sump.
Start the calibration, put the probe in the 7 and swish it around now and then for a good 5 minutes.
When the displayed number stops changing (should settle around 700), go on the 10 solution and do the same thing. It should settle at around 1000.
Finish the calibration and if it isn't good enough, do the calibration again. It may take several runs to get a good calibration.
If none of that works, you can try resetting your probe to factory default, and starting the calibration over from scratch.
Note that Neptune only recommends that this procedure be done on direct instruction from Neptune tech support.
However there's no risk of 'breaking' your probe or your Apex by doing this.
I and others have had success getting a persistently wonky probe to behave, with this method.
First, disconnect the probe from it's jack on the Apex head unit.
Then, run the calibration procedure. Don't wait for any values to change, just go through all the steps.
Next, reboot the Apex.
Now, plug your probe back in. Attempt manual calibration again, using fresh 7 and 10 solutions.