I really think that Jack, Ianto and the stopwatch is a red herring.

We just last week had Tosh hearing Ianto obsess over and over about Lisa and her death, and I don't think he's the kind of guy to fuck around with the boss to assuage his pain, particularly since I'm sure he's got unresolved anger about Jack not finding a way to save Lisa.

There's also the intercepted blog that indicates (to me at least) the idea that Jack isn't the kind of guy to take advantage of desperation or pain.