It seems like recent changes to the way flags are handled has introduced some strange behavior.
A little bit of background
Users who don't yet have the reputation to vote to close can flag for moderator attention, select "It doesn't belong here", and then select a close reason from the same set of choices available to close voters. These flags get added to the 10K queue, where they sit for a little while - if a 10K user agrees and votes to close, the flag is dismissed (as helpful) by the Community user. If nothing happens, the flag eventually "graduates" to the moderator flag queue...
And therein lies the problem
If a moderator responds to one of these "close" flags and closes the question without manually dismissing the flag, the Community user dismisses it as "helpful" and the moderator's flag handling count is not increased!
A few months ago:
I would expect the flag, once having been shown in the moderator queue, to behave as any other flag - action on the post that results in automatic dismissal also attributes the dismissal to the moderator who dismissed it.