Calibrating them separately is OK, but for that it is best to calibrate them separately while still using the FC. That allows you to set min=1000 and max=1900. RC radios usually put out closer to 1000-2000 which does not work with PWMSync (500Hz).
If you calibrate separately with RC, one small possibility is that maybe the stick was in a different place for this one than for that one, like the stick bounced off the end and you didn't notice it.
If you calibrate them with your RC radio, use PWM and 490 (or less if 490 doesn't work), not PWMSync.
If you calibrate them with your FC set to 1000 and 1900, even if you do it one ESC at a time, you can use PWMSync or any of the aforementioned PWM-numbers.
After calibration, do the neutral setting which is also described in the ESC calibration wiki article.