Firstly, make sure your step-up is relatively high (i.e. don't use the Body for Life aerobics 3-inch step blocks). This maximizes range of motion for the working leg.
Secondly, stand your non-working foot on tip-toes (full stretch) immediately before you start your working leg. This takes your potential energy contribution from your non-working foot to almost zero, thus allowing you to focus yourself into putting effort into the working leg only.