Performance in temporal difference threshold and estimation tasks is markedly less accurate for visual than for auditory intervals. In addition, thresholds and estimates are likewise less accurate for empty than for filled intervals. In scalar timing theory, these differences have been explained as alterations in pacemaker rate, which is faster for auditory and filled intervals than for visual and empty intervals. We tested this explanation according to three research aims. First, we replicated the threshold and estimation tasks of Jones, Poliakoff, and Wells (Quarterly Journal of Experimental Psychology, 62, 2171-2186, 2009) and found the well-documented greater precision for auditory than visual intervals, and for filled than for empty intervals. Second, we considered inter-individual differences in these classic effects and found that up to 27% of participants exhibited opposite patterns. Finally, we examined intra-individual differences to investigate (i) whether thresholds and estimates correlate within each stimulus condition and (ii) whether the stimulus condition in which a participants’ pacemaker rate was highest was the same in both tasks. Here we found that if pacemaker rate is indeed a driving factor for thresholds and estimates, its effect may be greater for empty intervals, where the two tasks correlate, than for filled intervals, where they do not. In addition, it was more common for participants to perform best in different modalities in each task, though this was not true for ordinal intra-individual differences in the filled-duration illusion. Overall, this research presents several findings inconsistent with the pacemaker rate explanation.