Here's some code I use to deal with this.
First we show the element, which will typically set the display type to "block" via .show() function, and then set the CSS rule to "visible":
jQuery( '.element' ).show().css( 'visibility', 'visible' );
Or, assuming that the class that is hiding the element is called hidden, such as in Twitter Bootstrap, toggleClass() can be useful:
jQuery( '.element' ).toggleClass( 'hidden' );
Lastly, if you want to chain functions, perhaps with fancy with a fading effect, you can do it like so:
jQuery( '.element' ).css( 'visibility', 'visible' ).fadeIn( 5000 );