'Place Windows' seems to be pretty buggy--when I had it on, it would make my windows jump to a screen-edge whenever they lost focus (or, with terminal windows, sometimes when I just hit return to the command line, which seems completely bizarre to me).
But with 'Place Windows' off, the start-at-0,0 issue is made worse when you have dual-monitors, with the one on the left below the one on the right; in that case, the 0,0 point is not actually on any monitor, so depending on the window size it might not appear at all.
If the window is visible, you can do a ALT-leftmousebutton on the window and drag it to where you want it. If you have dual monitors, you probably want to ensure that the left one is positioned at least as high as the right one.
That was my solution--turn off 'Place Windows', redefine my left monitor position to be as high as my right, and just manually place all my windows. I don't need to use the ALT-left thing because my panels are on my right monitor so I just grab the title bar.