Still fiddling with this, I've found that if you turn off the gate dialog which tells you how many passengers will board then you keep your custom sounds... for about 5 mins or so and then they stop working again anyway.  Ah well it is progress of sorts, my next attempt will be to downgrade my version of FSUIPC which will also fix the autopilot disconnect problem.

Also just a note about the KB article on custom sounds, reloading the aircraft doesn't seem to fix the problem for me.  Also while FSPassengers is in a flight it doesn't let you do that anyway.