I have this issue with fluxbox. It opens windows from time to time underneath the toolbar. I don't mean it maximizes windows below the toolbar, but sometimes when a new window program is started part of it is send below the toolbar. Does anybody knows how to prevent windows from going underneath the toolbar?

Alt+left mouse click grab window and drag it up. It should open again where you dragged it (I hope)

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Thank you rokytnji for your answer. Sure, one can always use that key combination to get around the problem and that's the way I do every time. I'd like to know a way to configure things so I don't have to fix the situation, though. I mean, i'd like to prevent this to happen.
BTW yes, window will open next wherever you dragged it.

By "send below the toolbar," do you mean, as if the application window extends below the bottom of the screen?

I have this happen with my netbook occasionally--not enough to annoy me into looking into it--and put it down to the netbook's screen geometry struggling with the application's expecting something else.

It's a long shot but you might try fiddling with your screen resolution settings to see if that gives you any leads.

If it's a matter of the toolbar covering up the application (or vice versa), you can check the "layer" settings in the toolbar configuration menu (right-click over an empty area of the toolbar for the menu).

Thank you frankbell for your comments. I followed your suggestion about the layer and actually modified the layer and set it to desktop. Now windows may cover the toolbar, but that doesn't bother me, as I am able to grab the window the usual way with the mouse.

Glad I could help!