There is currently a bug with the v13.0.49 Beta where Explorer replacement is not fully in place on Windows 11.
Using Win+E shortcut opens Windows Explorer instead of DOpus;
Using Show in Folder option in various programs opens the folder in DOpus at first but they also open a Windows Explorer window after about 15 seconds apart from the DOpus one;
Under Settings > Customize > Keys, is there anything for Win+E? If there is, try deleting it as it's not usually needed to intercept Win+E on current Windows versions (10 & 11).
Same here with Beta 13.0.49 . Win+E always opens default windows explorer. Tried all settings you wrote here, nothing worked. @Leo No, there is no Win+E in Customize - Key
I have "Open the Default Lister" for double-clicking the Windows desktop activated. This still works perfectly.
It's working OK here on Win 11 (just updated to latest normal release; not using Insider builds) and Opus 13.0.49.
Although, interestingly, the first time I used Win+E it opened File Explorer, after that it opens Opus every time.
It's possible a component involved has had its registry settings damaged. Re-running the latest Opus installer would fix that if it's the case.
If Opus has been launched elevated, that could also cause a problem. (But that doesn't look like it's happening, from the screenshots above, as you'd see a warning on those Preferences pages if it was the case.)
Changing the "Open File Explorer to" dropdown in Explorer's settings could help if something has made it open a different initial folder. (Mine is set to "Home" but also works with the only other option I see, "This PC".)
It's also possible another program is intercepting Win+E and blocking Opus from doing the same.
I downgraded to 13.0.46 where Win+E worked fine. Then I upgraded to 13.0.49 again, and Win+E works fine again. This is strange but working. And I have no other intercepting apps running.