Anything out of whack isn't working quite right. If a math student's basic formulas are out of whack, none of her answers will be correct.
If your computer is out of whack, it isn't doing what you need it to do. An out of whack kitchen scale will give you the wrong measurements. And, if you twist your ankle, it can throw your whole body out of whack. This adjective phrase implies that things are out of balance or unaligned in some way. Out of whack is also the opposite of the now-obsolete in fine whack, which meant "in good condition" during the nineteenth century.