A.R. 3-3-5-VII says that if an injury and a media time out are combined, the play clock is set to 40, so I'd say that it is set to 40 any time there is only a team B injury.
Kalle, in that AR, the only reason the clock was stopped was for the injury, so, following the media time out, the game clock (and play clock) would start on the referee's signal. That's why 40-seconds is unquestionably proper in that AR.
But, as Brockton notes, there is minor ambiguity regarding scenarios in which the game clock was stopped for other reasons. Team B gains no clock advantage if the clock would not start until the snap (e.g., incomplete pass, BC/ball out of bounds with less than 2-minutes in half), or not at all, as in the case of a Try. Allowing the 40-second rule to supersede makes it simple, although a bit nonsensical in some scenarios. I doubt anyone would even notice if you used 25, in either case - certainly not on a Try. As silly as it may be, though, I would use 40, unless and until Shaw issues something that says otherwise.