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Update:
It seems that when I go to preferences, the 'domain' value being passed in the query string is the URL instead of the domain ID:
http://www.example.com/modules/multisite/admin.php?fct=preferences&op=show&confcat_id=1&domain=http://example2.com
If I replace the domain value with the domain ID then I am able to edit the preferences.
New problem, though, I can edit preferences only for the first domain listed. If I try replacing the domain value in the query string with 2, it still brings up the preferences for domain 1.