Alt-clicking the close button makes everything disappear from my desktop

When alt-clicking the red close button on a standalone TotalFinder window (to get the window size/position remembered for the next new window), all icons disappear from my desktop. They still appear in a TotalFinder window, just not on the main desktop display.

Also: although the alt-click does cause the window size to be remembered, it’s forgotten again when I open a TotalFinder visor window. Then the next standalone window is reset to a (default?) square shape.

OSX 10.9.3, TotalFinder 1.6