Update. I resolved the issue!
Initially, I had this at the end of my 'headinclude' in vbulletin:
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<link rel="shortcut icon" href="favicon.ico" />
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I changed it to this this:
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<link rel="shortcut icon" href="http://www.domainname.com/favicon.ico" />
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Now the favicon appears for all my subcategories, etc. Yay!