I have a Beta Factory , you are not alone in the fight against water in the box .
It is a problem with the bike , deep water , it will find its way in .
I have spoken to Beta owners many have had or have the problem .
I have done the following to cure it .
Front fender mud extender
Plastic guard that runs up the gap between the silencer and air box
Plastic clear filter cover , it is not for the latest Evo models but its easy to make fit , I had to drill a few holes in it to allow enough air in , obviously holes allow water in but its harder to get through !
Ram water filter sponge in all the gaps round the air box , shock area etc ( it still gets enough air )
Tape over the hole where the electrics are stored
My secret weapon , I have velcroed a super absorbent pad into the bottom of the box . This soaks up anything that might get passed all the other defences .
I have tested to extreme by splashing my way through deep water , all the above did the job !