It has always worked for me. Are you sure you are in a legal e.p. position? 
"en passant"
remember u can only use that move when your pawn is on the 5th rank and your opponents pawn to the left or right is still in their starting postion , then ur oppnent jumps one of these pawns 2 spaces forward passing over your attack square on your next move you can use the en passant (must be down right after the double space jump by oppenents pawn) , if your oppenent first moves his pawn one square and then to the second you can not perform en passant because he would have challenged your pawn and ofcourse you cant en passant if it would cause ur king danger, i rarely use the move but im always on the lookout for good opportunitys to use it
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I have tried to use an "en passant" move quite a few times during my games but it doesn't allow me to. My opponents are able to use it all the time. Is there some special button I have to use to let the move go through? Pretty frustrated with the whole thing. Any help would be greatly appreciated.