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When I save my startup file using either Ctrl+U or File -> Defaults -> Save Startup File, the next time I open Blender, the original startup file opens.

I'm using Blender 2.82 on Ubuntu 20.04, and I downloaded Blender as a snap.

I'm assuming the issue is that the actual blender startup file isn't located at ~/.config/blender/2.82/config/startup.blend. When I look at this file manually, it is changing, and when I open it with blender, it is the file I'd like to open at startup, but this isn't what opens at startup.

Assuming that I'm correct, and it's actually using a different default location for the startup.blend, I searched for the file it's actually opening. There are startup.blend files that exist in the following locations, but they don't appear to be what it's opening:

/snap/blender/37/2.82/scripts/startup/bl_app_templates_system/2D_Animation/startup.blend
/snap/blender/37/2.82/scripts/startup/bl_app_templates_system/Sculpting/startup.blend
/snap/blender/37/2.82/scripts/startup/bl_app_templates_system/VFX/startup.blend
/snap/blender/37/2.82/scripts/startup/bl_app_templates_system/Video_Editing/startup.blend

At this point, I'm either wrong about what the problem is, or I need to tell blender where to get its startup.blend from.

Blender is located at:

$ which blender
/snap/bin/blender

So the question is: How do I edit my startup file, so that it holds the configuration, since the default doesn't seem to work?

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You need to select the default settings (like whether to import previous keybindings, theme, etc) on the first splash screen, then you will be able to set your default file.

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