This is nothing but a little annoyance I had from day 1 with Mabox.
As the title says, QT based apps (I don’t know why) always open behind the Tint panel.
The only workaround is to press Alt-F6 and then it goes back to normal. Regular apps, on the other hand, never do that.
The easiest example, if you want to try, is Foxit Reader. Any advice please? 
Try to change panel layer to bottom in your tint2 conf file.
panel_layer = bottom
They should go above panel then - instead of behind 
Thank you.
It kind of works but now is covering the Tint panel. Still needs Alt-F6 to put it back in place. 
I’m closing this bug.
Further testing with other QT Apps (ie, Virtualbox) show them fine. I was trying to find possible causes (problems) between GTK and QT interactions with Tint2 like this scenario but nothing solid came up. Then suddenly hit me: maybe this is a particular issue with Foxit Reader.
Lo and behold, found it right away. 
Will try harder next time before posting.
