Try unpinning the left icon, then pinning the right one. That may fix it, if the Taskbar is confused.
Another possibility is a script add-in is installed which is assigning some Opus windows to a different taskbar group. (Settings > Preferences / Toolbars / Scripts to check which add-ins are installed.)
I closed the right icon (the unpinned one) so that only the pinned one (on the left was there).
Next, I used the pinned icon to start up a new Opus instance.
An unpinned icon showed up on the right. Hovering over the pinned icon only shows the two instances. Hovering over the unpinned icon shows the new instance
I launched a few more Opus instances using the pinned icon. They all show up when hovering over the unpinned icon on the right.
Very strange. I am pretty sure I've seen this behavior before but never connected the dots. I don't think it is new to the latest release.
By the way, Opus is one of the best utilities I've ever used.. by far (best thing since sliced bread!).. can't imagine ever going back to a vanilla file system explorer.