Most likely it is due to a different CSS Style getting precedence during the effect. See http://jsfiddle.net/qhK96/1/ where the background turns red during the shake animation.
div > input /* while not in animation */
div > div > input /* while in animation due to wrapping from jQuery, like ElendilTheTall said */
Solution is easy: Fix your css. Sounds a little smartassy, sorry, but we would need more info to point you to your problem. As a first try add !important
to yout style definition height or try setting height with line-height.