One of the problems with the use of mobile phones within aircraft occurs when the handset is first switched on. The phone sends a ident message on maximum power. Agreed, maximum power does not amount to more than about 2 watts but the potential for interference to aircraft systems is always there. Particularly if the handset is not functioning correctly.
Under normal circumstances (for example on the ground) the local cells which are in range will then send acknowledgements. Handshaking takes place to establish the nearest cell and the minimum amount of power necessary for communication.
If a jamming system is installed in an aircraft it would have to not only jam signals, but also prevent the handset from sending these high powered data pulses.