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This is usually caused by OmniWeb not shutting down properly. If you are sure you're only running one copy of OmniWeb (logging out and then back in insure this) then remove this file:

~/Library/Application Support/OmniWeb 5/HistoryIndex.ox.lock

This wont delete your history index (which provides the full text search available for your history) Just a lock file that prevents multiple copies of OmniWeb to use the index at once.