Both points of view expressed so far are valid. And, of course, I've never seein it specifically addressed in any of the mercy rules (no one ever thinks that far in advance). So, I think it depends on the wording of the rule.
If it says "the clock stops only on a TO or injury" then start it when the clock would normally start.
If it says "the clock runs, except during a TO or injury" then start it when the TO is over.
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