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BUT when I go to github.com and check it's not up to date. What I have to keep doing is going to Github Desktop and click on "Push origin" in order for the commit to show up on github.
That's out of my pay grade. Unless you can find someone who understands this better than me I would go through the Issues log at https://github.com/denolehov/obsidian-git, see if any fit your problem, if not then raise a new one. The plugin is coming across a problem that the developer has not yet coded for. They may be able to quickly identify the issue and either fix it or let you know what you need to do to work around it.