Yes I can see how that would make sense, but if it were being started using engine generator power on the busses and not just the battery would it make any difference? That the battery gets about the same amount of cooling in flight (I assume as the equipment cooling fan works in both) as on the ground would make this understandable for the time limitations between start tries. I was also under the impression that the limits were due to heat built up in the APU itself during the failed start attempt. We got to talking about the air flow past the intake and that in flight the flow into the intake for the APU might actually be less due to it tending to flow right on past the opening if you will. I would think then the limits would be greater in the air than on the ground except that my previous employer had it as no time required between start attempts while in flight.
Thanks all for the answers thus far and keep them coming as I am and could still learn something. Until I can find something from Boeing them selves as to weather the limits apply in flight or not I will keep looking for the exact answer to the question.