Created attachment 4278 a screenshot illustrating the problem: Settings Manager's title bar is obscured by a panel I prefer to have two horizontal, permanent (that is, not automatically hidden) panels at the top of the screen, the topmost one containing mostly launchers for frequently-used applications, and the other one containing mostly the window buttons. I've configured the first panel to be 32 pixels wide and the second to be 24 pixels wide. When I open new windows, most of the time the appear entirely in the background area, but once the screen has a few windows, some new windows are created in a position where their title bar is obscured by the second panel. I can't grab them by the obscured title bar, but have to drag them down using the alt-left click combination. See included screenshot, which shows the situation where I've opened the Settings Manager when there are already several windows on the desktop. I've circled the problem in red. The icons shown by default on the screen (home screen, etc.) are also too close to the second panel. It appears that the fact that there are 48 rows of pixels that are reserved for panels isn't taken into account by whatever part of the xfce software needs to take it into account. (I was only guessing at the correct component under which to report this; sorry if I got it wrong.)
I forgot to note in the bug report that whenever I maximize a window, the same problem occurs. You can actually see this in the screeshot; the Fraqctive application is maximized, and you can see its menu bar just below the bottommost panel, but its title bar is obscured by that panel.
I found a workaround. I replaced the two panels by one, and added a separator with the New Line style to it. This makes the one panel separate the items into two lines, and now it looks like the windowing system doesn't become confused about how much vertical space is available to it. There's still the drawback that I can't set the widths of these two lines independently, which I could do when using two separate panels. (By the way, my arithmetic was off in the original bug report: 32 + 24 = 56, not 48. Still, the point stands.)
A workaround I found that works at least in Xubuntu: Go to Settings -> Workspaces, and change the top margin to the total width of the top panel or panels -- or, if you have your panel on some other edge, change the width of the margin on that edge, of course. This prevents the windows manager from putting windows under the panel(s).
I have a single vertical panel on the right side of the screen (2 rows, 40px size each) and maximized windows go behind it every time. The "don't reserve space on borders" checkbox is not checked. Weird enough, it seems to work when I add extra horizontal panels, but not with the verticals ones. This has started ocurring in 4.12 for me, it was good before.
It seems my issue has dissapeared after latest xfce-panel upgrades... :)
This can't be fixed properly because "floating" panels (i.e. not attached to a screen edge) don't set struts. Solution: Use a single panel with two rows.