A surprising red (-1) appeared on my inbox counter: 
I decided to mark one message as unread and then the counter marked Refresh (0): 
When I marked a second message as unread, the counter marked (1): 
Q: How to get rid of this shift?
A surprising red (-1) appeared on my inbox counter: 
I decided to mark one message as unread and then the counter marked Refresh (0): 
When I marked a second message as unread, the counter marked (1): 
Q: How to get rid of this shift?
There was a revamp to the inbox about a year ago, and I've been having similar slips happen from time to time since then.
Generally I find that hitting "Mark all as read", (even though I don't see anything marked as "Unread"), clears it up. Have you tried that?