it varies between 999.9 and 999.2
0.7% is not bad at all.
two things
1) integrate 8 or 16 readings
2) do not change the display unless the chnage is > your stated resolution/precision.

To get a 'rock solid' reading of a frequency is impossible. Using an interrupt you have the variance from completing previous instruction, using a PLL you have thermal variations and synch variations.
So, you need to fool the display by either of the above means.

Erik