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When you say "monitor all branches", the plugin thinks that means "if a previously unbuilt SHA1 is detected on any branch, then compute the differences between the most recent build and that unbuilt SHA1 and pass those differences through the inclusion and exclusion filters".
There is an option in the plugin to make comparisons to a specific named branch, rather than to the last build, but I'm not sure if even that would meet your needs.
You might try a different experiment, using the multi-branch plugin to automatically create and delete jobs for branches as they are created and deleted. I'm not sure that plugin allows inclusion / exclusion, but it is probably worth an experiment.