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My workaround for the left click/focus issue with Hulu desktop was to go into RB settings, mappings, the under the Hulu desktop behavior set an unused remote key to emulate virtual mouse left click. I chose "Select (held)" and assigned it to virtual mouse, left double click. Single click wasn't always working for some reason.
Not a solution per se but a work around that doesn't require physical keyboard or mouse to be involved. Once Hulu loads up I press and hold the select key on my remote for about 2 seconds and after the left clicks are emulated all is well.