When I search for users using "Inactive users (Haven't posted anything)" condition through the admin panel, the members listed have Total Number of Replies as 1 in their listing, even though they have not made any replies. However, when I search for the same users using direct query of their username, the Total Number of Replies is shown as 0.

I'm not sure why it's happening on your forums, but on my local copy of miniBB, as well on our live forums and test forums I can't repeat the same. I also see that the function which gets numbers of posts in those lists, use the same value from the database, so it's difficult to understand where the discrepancy happens.

Make sure you have the latest version of bb_admin.php file as it's presented in 2.2a.

Yes I rechecked. It's from 2.2a itself. However, it's not a major issue and hence I'll let it pass.

Actually is this happening just for this user or for all users?

Can you check what is the value for this user in users table? I mean num_posts column.

It's happening for all users. But when I check for individual users searching for their username, then their reply count shows as 0.

Just get me in touch privately providing your FTP as always :-) Without debugging your copy of script I have no ideas.