QT includes a class called QSettings, which stores a settings dictionary in a platform-transparent way. QT4 on *nix puts the settings in INI-style files under the directory ~/.config.
It so happened that I had a file called ~/.config in place, so QT couldn't create the directory. As a result, my new PyQt4 development tools lost all their settings every time I closed them. That's slightly annoying with the QT Designer; extremely annoying in the case of Eric4, which comes with more preference panels out of the box than Eclipse. In both cases, settings were lost in a completely silent way. There was no error message, not even on stderr. The only indication anything was wrong came the next time I ran the application, as it started with factory settings once more.
Luckily, since I was writing a QT4 application myself at the time, I could quickly look up the QSettings docs, find out where the settings were supposed to be saved, and diagnose the problem. An ordinary user of a QT4 application, however, would have had to resort to online support of some kind.