jquery fadeIn leaves opacity at 0

Some CSS is overriding your div when it is hidden..Better add the opacity style to your div as 1.

Else do,

$('#MyDiv').css('opacity','1');

After your fadeIn call...

Try jQuery .fadeTo function.

.fadeTo( duration, opacity [, callback] )  
.fadeTo( duration, opacity [, easing] [, callback] )  

Sample:

$('#book').fadeTo('slow', 0.5, function() {
  // Animation complete.
});