It seems to be a problem occurs when using CSS3 transition with IE11.
The problem is resolved by disabling CSS3 feature of Flexslider:
useCSS
useCSS allow users to override using CSS3 for animation. Translate3d still has numerous bugs that can crop up and wreak havoc, so this is a great property to play with if you are experiencing unexplainable issues in Webkit browsers.
Just testing whether browser is IE11, and passing useCSS: false
to jQuery.flexslider(), it solved.