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I just found out that I have all kinds of duplicated shortcut entries in my preference window. Is this normal? I tried to delete the duplicates, but what happens is, the actual hotkey gets deleted as well. And whenever I delete one, it always scrambles the order of it. No way of knowing which one is the actual.

I hope there is nothing to be concerned. I do not notice any problem while working on models.

user preferences shortcut list showing the duplicates

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This looks like an addon problem to me. For ⇧ ShiftQ you have entries for call menu and call pie menu. I would say you have multiple addons adding the same shortcuts, or you have more than one copy of the same addon with different filenames. It could also be an addon that does not unregister itself properly leaving the shortcuts behind after you disable it.

An install of blender includes an addons folder that contains the official addons, then there are 3 places blender looks for data files, You could have a scripts/addons and scripts/addons_contrib in each location that can contain the same addon, if the same addon uses the same filename you will get an error saying you have duplicates, but it is possible to have the same addon saved with different filnames that can register without error and create the duplicate shortcut entries.

Expanding your duplicate keyboard entries will show the operator/menu name used by the duplicate which can give you some idea as to what addons are causing the problem. If the addon is not obvious by the name, the operator or menu name used for the shortcut can be used to search through files in the above directories to find where it originated.

shortcut entry

If the name is two words separated by a . then this should match the bl_idname of the class used -

class CLIP_PIE_marker_pie(Menu):
    # Settings for the individual markers
    bl_label = "Marker Settings"
    bl_idname = "clip.marker_pie"

If you get a name like CLIP_PIE_marker_pie then it may match the class name or only part of it (the later part most likely) in the file. This is also an indication that the addon has been disabled but has not cleaned up it's keyboard shortcuts.

After finding and removing any duplicates you may also need to disable duplicate addons and remove duplicate shortcut entries, then "Save User Settings" so they stay disabled next time you start blender. You could also use File->Load Factory Settings, re-add your personal adjustments and then Save User Settings to get a clean start.

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Update my old post

There is not much can be done to this. It's just a glitch where every time I save the hotkey settings to a profile, it adds all the existing ones on top of the new ones. It could be due to all the plugins I installed.

My dumb solution to this is just to map a rapid left click macro on one of your gaming mouse button, then click through each individual checkbox in front of the entries. The duplicate ones will disappear once you click on it. Re-enable the ones you want to use after, and do not ever press the + button on the key config profile list. I think whatever changes that's made is automatically saved in that profile when it's set. There is no need to click that + button at all.

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That looks like a pretty strange set of keyboard shortcuts, they look rathr irregular and nothing like my 3DView (Global) settings. Very different from what I have, and searching for operators I find non of what you have listed there.

Are you using the default Blender Keymap or one of the custom presets. Did you customize your own set of keys yourself?

Do you have any addons enabled (like Pie Menus, or Node Wrangler or any others)? Those may be key entries defined by addons that override default built in shortcuts, to add new functionality and launch new menus. Try disabling any addons and see if they go away.

If you have no problems your probably shouldn't worry too much.

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