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35a32c5
(Get the code!)
Thank you for looking into this.
I tried xprop on Terminator (from Fedora repo), nautilus, qtdemo-qt4, glxgears, xeyes, and kompare. I also saw that there's an experimental gtk3 series of Terminator, so I got that (bzr branch lp:terminator/gtk3), ran it, and used xprop on that too. Terminator always had the no-appearance problem, including the gtk3 version, and no other windows had the problem, including the QT4 and KDE ones. I've also run Geany and SpeedCrunch, and some things not in the Fedora repos including HipChat and Yubico Authenticator. Terminator is still the only one with the problem.
xprop outputs are attached.