Here's what I see. I think I'm doing basically the same thing, but it appears to work OK for me.
This is with Update folder sizes after file operations where possible turned off, but I also tried with it on afterwards and saw the counts still update after a refresh. (Some would update before a refresh, but not all.)
The Refresh button I'm clicking runs this, in case your button/hotkey is different:
Go REFRESH=source
Let me know if you can see any differences or think of anything for me to try.
Another possibility is that there's already an outstanding calculation for the folder/tab which is stuck or taking a long time. That might prevent new calculations starting, although it'd usually mean you don't see any counts at all after a refresh, not that the old counts would be kept. I'd be surprised if it was that, but a process snapshot made when the problem is occurring would show if it is. (Only one would be needed, not multiple as normally are.)