I had a problema that you can have too and to my knowledge there is no reason for this.
The ignition modules are done by Ducati, I flew my plane and nex day when I tried to start it both modules failed to provide a spark, both where totally dead, I checked all the wires, connections, etc. etc. and everything was perfect.
In one fórum I read that somebody in Germany had the same problema and the Rotax mechanics and the tecnicians at Ducati didn´t know the cause but for my surprise they heal again by itself when they ran at over 2000 rpm so I did the test and it really works!
I removed the A module and left the bad B module and installed a borrowed A module from a friend, I started the engine and it fired! at over 2000 rpm I turned the switch of the module A off and it was running on the module B, then I switched the A on again and switched off the module B and like magic the module A was working again!
Then I installed my bad A module and started the engine with the good module B, after the engine run at over 2000 rpm I turned the module B off and also my bad A module was running again.
After this in the magneto test when I did the test of both magnetos I have a drop of only 100 rpm at each magneto and since this day I never had a problem with the ignition modules.