Permutation entropy (PE) has a growing significance as a relative measure of complexity in nonlinear systems. It has been applied successfully to measuring complexity in nonlinear laser systems. Here, PE and weighted permutation entropy (WPE) are discovered to show an unexpected inversion to higher values, when characterizing the complexity at the characteristic frequencies of nonlinear drivers in laser systems, for output power sequences which are pulsed. The cause of this inversion is explained and its presence can be used to identify when irregular dynamics transform into a fairly regular pulsed signal (with amplitude and timing jitter). When WPE is calculated from experimental output power time series from various nonlinear laser systems as a function of delay time, both the minimum value of WPE, and the width of the peak in the WPE plot are shown to be indicative of the level of amplitude variation and timing jitter present in the pulsed output. Links are made with analysis using simulated time series data with systematic variation in timing jitter and/or amplitude variations.