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My apologies - I thought I was on the latest version but it seems like I must have dismissed the update dialog at some point and then it didn't show up anymore.

Please upgrade to the latest version of WinSCP.
I believe this has been fixed in 5.16.1:
Bug fix: After directory comparison before synchronization finishes, task bar button still shows a progress bar.

WinSCP 5.16 Beta (Build 9865) on Windows 10 x64 Professional (1909)

I have attached a screen capture demonstrating the issue. As you can see, the taskbar status remains even after closing the dialog.

Re: Taskbar status not updated if no differences are found during sync

I cannot reproduce the problem. What version of WinSCP are you using? Can you post few screenshots?

Taskbar status not updated if no differences are found during sync

Steps to reproduce:
1. Synchronize a folder (local -> remote or remote -> local should not matter)
2. The taskbar shows a green animation while differences are being searched for.
3. If the result of the synchronization is that no differences are found, a dialog is shown to inform the user, but the taskbar animation keeps running until the next event that updates the taskbar animation (e.g. uploading a file)