Multiplex PCR, shorter amplicon inhibiting longer amplicon?
It turns out that the $T_m$ was in fact the issue, or rather, that the computation algorithm overestimated the $T_m$ of the primer pair for the longer amplicon (or underestimated that of the shorter one). At any rate, it seems that at 60°C the shorter amplicon primers hijack the polymerization mechanism.

Setting the annealing phase temperature to 55°C solved my issue, and now I consistently get better results: