User Settings Seem to be Saving Randomly

When I start Blender fresh, or click File->New, the default scene it brings up tends to be a few autosaves back of whatever large project I’ve been working on recently.

What I’d like as a default is the empty scene with the cube from the factory settings, but with my user preferences, ops and key bindings set. I’ve saved such a state with Ctrl-U, but despite my avoiding hitting Ctrl-U anymore, it keeps getting overwritten with whatever I’m working on and I’m not seeing a clear pattern as to when and why.

So I’m wondering what else besides Ctrl-U keeps saving over the default user settings.

Strange problem, maybe you are clicking the save user settings option in the file drop-down when you intended to click user preferences or load factory settings.

I don’t think so; I always use keyboard shortcuts for those, and rarely click “Load Factory Settings”. In any case, saving user settings brings up a little confirmation window you have to click, so I’d notice.

To be honest I have no idea how to help you, to answer you question though, as far as my knowledge goes, ctrl-u is the only (default) hotkey for saving user settings. did you check that hotkey to see if it was entered correctly or that there isnt an extra hotkey conflicting?