Selgas
Two point possibly:
1. Have an expert check the pipesizing feeding the gas supply to both appliances and at the same time have the pressure settings checked – it is possible that an undersized/underpressured installation can cause this problem.
2. Introduce a source of free air to the room in which these machines are installed to prevent the combustion fan from “sucking out” the pilot light on the water heater when it is running.
Personally I would get the services of a proper gas expert to come check it out – it all sounds a little weird. Better not to muck with it yourself get an expert involved – a little money spent now will prevent a disaster in the future.
Remember: Don’t muck with gas appliances and the result of someone not qualified to play with them often leads to a dangerous situation for all concerned. 
Selgas Services Ltd
Craftsman Gasfitters, Plumbers, Electrical Service Technicians
