I am not aware of an issue with that in PokerTracker 4. For example here is a small sample of hands for a player:

- flop_actions.PNG (17.62 KiB) Viewed 659 times
Flop AFq (including checks) on that sample would be:
(6 / 16) * 100 = 37.5%
Here are the results in PokerTracker 4 and Hand2Note for that sample of hands:

- afq.PNG (19.7 KiB) Viewed 659 times