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Transient problems

Dialogs appear in the wrong frame or alone as a new main window instead of at the bottom of another window that the dialog is supposed to have sprung from.

Again, blame the program in question for not setting the transient_for hint correctly. You should ask the authors of the program in question to fix it, but in the meanwhile, you could experiment with the transient_mode winprop. (Note that Ion does not and will not support the “Extended WM hints” brain-damaged in-violation-of-ICCCM multi-parent transient notion.)