I'm just leaving a note here if someone comes up with a similar problem as I spent a lot of time figuring it out.
I had a similar issue when running the remote as a service but with a different fix:
When the Service ("Bamboo Remote Agent") is created, it is created as the "Local System" user, instead you need to change it to your PC account user (the one that Git is linked to).
To do this just go to Windows Task Manager in the Services tab and on the "Services..." button in the bottom.
Right click on the "Bamboo Remote Agent" service and select Properties then in the "Log On" tab Log on as: this account...
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