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If a subsite is configured with an empty pages text area at admin/build/subsites/1/content/pages and the option "Show on only the listed pages." is chosen, then that subsite will be activated on the root of the site.
At first sight, checking if $subsite->pages is empty in _subsites_get_current_by_pages() will solve this issue.
Comments
Comment #1
Cyberwolf CreditAttribution: Cyberwolf commentedComment #2
davyvdb CreditAttribution: davyvdb commentedAfter checking offline with Cyberwolf, this appeared to be a bug in the specific installation.