The Madden Julian Oscillation (MJO) is a prominent mode of tropical variability and a key driver of intraseasonal predictability. Accurate prediction of the MJO is challenging due to complex interactions with the background state and sensitivity to initial conditions and unresolved processes. Using NOAA’s Unified Forecast System, we explore the impact of subtle differences in initial conditions on MJO forecasts over the Indo-Pacific. Model runs initialized with two independent reanalyses show significant and systematic differences in MJO-circulation amplitude that persists over a 15-day forecast period. Additional analysis attributes this to differences in their initial atmospheric static stability. The reanalysis that is initially less stable is associated with enhanced large-scale vertical motion and divergent winds throughout the forecast. Notably, a convection-based MJO index shows less sensitivity to initial conditions, suggesting that variations in convection and diabatic heating are not the main drivers for the predicted differences in MJO circulation amplitude.