Using 12.3.3 too.
Some screenshots for the z-order convert-issue, it's 100% reproducible, at least on my machine here:
Use any image file and make sure that the target format already exists, like this:
Open the convert dialog:
After confirmation, Opus detects the overwrite conflict, but dialogs pop behind the lister. The only indicator is the yellow progress bar on the bottom:
If you click on the yellow bar, this bring the dialog boxes to front, but still in wrong order. You can see that the replace confirmation is behind the progress window. It think it is intended that this should be the uppermost window because it's the only one you can control in this state.
If I click on the overwrite confirmation window, it comes to the front, but the progress bar window is now behind the conversion dialog. If I open the system menu of the progress bar window it's getting even more weird. You can see that in the screen shot:
I can still use the function, the sorting is just very odd.