Probably the problem is caused by the win build storing its preferences in the program dir (I think) instead of the home dir. I will now commit a fix which you'll need to test on windows. I'm not sure g_get_home_dir() works on windows, but if it does, it's the correct way to solve the problem. It should return the dir in your $HOME environment variable, and if there's none, I think it will return C:.
Committed. Now the win build is supposed to store prefs in $HOME/.inkscape/preferences.xml so it stays unchanged when you upgrade the program. Please report if it works or not.
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