This bug is so weird I suspect that it may be something wrong with my install or at least just Debian, as I couldn't yet find many people reporting the same issue, while searching for it.

What happens is that Inkscape will change its preferences just normally while I'm running a "session" (i.e., while I have a running stance), it will save the preferences.xml accordingly when I close all instances, but as a open a new "first" one, it will overwrite preferences.xml with defaults

I'm using debian testing/wheezy, and I've tried inkscape versions from stable, testing, unstable, and experimental. And some ubuntu version (still on debian).

Tried also deleting the whole .config/inkscape folder, and trying with a different user.

The same doesn't happen if I overwrite default.svg though, it will preserve such default document settings, and nothing else.

I've just noticed an interesting aspect. In the openbox desktop environment, which is the one I regularly use, inkscape's settings will be reset at every new "inkscape session" (that is, it preserves altered settings for new instances while a previous instance is running, but a new "first" instance, after all others are closed, will have default settings). But on KDE and GNOME it will preserve altered settings even after I close the last instance. Frustratingly, it won't restore such settings after a new KDE/gnome session.

I wasn't expecting that the DE would make such a difference, even though I'm not sure it's really related, perhaps KDE and Gnome, both more "robust" don't really clear some memory/cached files even though the program was closed, but they don't really have any real advantage in the "core" issue with the file being rewriten at some point. But I really don't know. Now I'm not sure it's an individual-install issue, inkscape issue, or DE issue, with varying degrees. I'll see how it goes on another machine, as soon as I can.