I have noticed recently that flags I have raised are not reflected in my flag count. I have been attuned to it especially since I am approaching a badge. It seems to be frozen at 177 since early June, but I know I have raised a few since then, and through some research, find that they have not increased my count. Noticeably, this one from just an hour ago is also not reflected. Can someone research that the operation is still there and properly functioning?
In the hopes of not revealing any sensitive information here (but you asked anyway), there is no flag from you recorded for that linked question at all. Likewise does none appear in your list of flags. So according to the system you did not flag that question and if you say you did, then something's awry.
However, you did close-vote that question. So could it be you are mistaking close-votes for flags? Since you have full close-voting privileges your close-votes are actual votes and not flags, in contrast to low-rep users who can only flag but not vote. Even if you explicitly use the "flag" link and try to issue a close-flag, it will automatically redirect you to the "close" dialog, since you should have chosen that in the first place. You have the privilege to issue proper close votes and thus also the obligation to do so responsibly, there is no way to raise a close-flag as a kind of "less binding close-vote".