Before you uninstall/reinstall the engine, check the common UCI settings. (Engines --> Manage --> UCI). There's a setting for "Common max CPU cores". My guess is that it's set for 1. Changing that number will change it for all engines. If you disable that setting, then you'll be able to change the setting in the Stockfish configuration window.
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I am trying to add threads so that my calculations go faster. But when I go to confingure the engine, I don't see a selection to change the number of threads. Is this a Stockfish 7 thing or an Arena 3.5.1 thing? I have always been able to easily adjust this in older versions of Arena and Stockfish.