The Inter-Pulse-Interval (IPI) of heart beats has previously been suggested for security in mobile health (mHealth) applications. In IPI-based security, secure communication is facilitated through a security key derived from the time difference between heart beats. However, there currently exists no work which considers the effect on security of imperfect heart-beat (peak) detection. This is a crucial aspect of IPI-based security and likely to happen in a real system. In this paper, we evaluate the effects of peak misdetection on the security performance of IPI-based security. It is shown that even with a high peak detection rate between 99.9% and 99.0%, a significant drop in security performance may be observed (between -70% and -303%) compared to having perfect peak detection. We show that authenticating using smaller keys yields both stronger keys as well as potentially faster authentication in case of imperfect heart beat detection. Finally, we present an algorithm which tolerates the effect of a single misdetected peak and increases the security performance by up to 155%.