When updating your repository password, SourceTree doesn’t completely remove the old password. It will continually try both the new and old passwords automatically in the background when trying to authenticate with your repository.

To use only your new password, you need to manually remove the old password from:

~\AppData\Local\Atlassian\SourceTree\userhost
~\AppData\Local\Atlassian\SourceTree\passwd

And double check SourceTree’s application settings in:

Tools > Options > Authentication 

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