System allowed my opponent to perform a
queenside castling going through a box in 
check. This has already happen in the past.

As the International chess rules said 
here

http://www.fide.com/component/handbook/?

id=124&view=article

''2) Castling is prevented temporarily:
if the square on which the king stands,
or the square which it must cross, or the square which it is to occupy, is attacked by one or more of the opponent's pieces''

Here is a screenshot

http://i.imgur.com/Oc9cjsU.png