I like to keep my Programs lists in some order... so I move program folders, after I install them, into subfolders.
If I update/reinstall an existing program, then when I open Classic Shell, Start, Programs lists... the program folder appears in (All) Programs again, so I move it to the subfolder I wish, again...
...whereupon Windows finds the previous folder already there and pops up a window asking for confirmation to Replace/etc... but the confirmation window appears -behind- the already open Classic Shell Programs lists. If I'm lucky, a piece of the titlebar is visible so that I can move it out from behind; if I'm unlucky, the entire window is behind the Programs lists... and while I can Alt-Tab to view it, as soon as I let go of Alt-Tab, Program lists return to the forefront. I have to go to Taskbar, find the Explorer icon, right-click and Close it, terminating my folder move.
What version of Classic Shell and what version of Windows?
Windows 8 Pro & Classic Shell 3.6.2
It's that nasty bug again in Windows 8 which also happened when you go to delete an item from the menu and it made the dialog appear behind the menu, so Classic Shell had to be modified to close the menu so the dialog shows. :(
Try this post again...
So... I take it that there will be a fix, yes?
I will look into it, but no promises. The problem is that for some operations it is best to close the menu and for some it is best to keep the menu open. It is hard to know in advance which is the case.