It might not even be a Whatsapp problem. It was working fine when I first installed Windows Phone 8.1, I was even impressed at how fast the notifications came through and then suddenly it stopped working.
Remember some months ago, way before Windows Phone 8.1 people were having issues with Whatsapp and it was something to do with the Windows push notification servers, when Microsoft fixed it the notifications went back to normal. My brother's Windows Phone is still on 8.0 and his notifications are fine.