This paper presents the results of unsteady Lattice Boltzmann simulations of the JAXA high-lift configuration Standard Model (JSM) in the JAXA Low speed Wind Tunnel. The study is a part of a continuing collaboration between JAXA and Dassault Systèmes and focuses primarily on understanding the differences between free air and wind tunnel simulations of the JSM half-span model. First, the effect of simulating with a boundary layer transition model as opposed to having a fully turbulent boundary layer is presented. The influence of the standoff alone, followed by a detailed analysis of the entire wind tunnel to investigate wall interference effects is discussed. Finally, the impact of including the wind tunnel geometry on cases with and without the nacelle chine is presented. The paper also addresses some of the open challenges faced when simulating high-fidelity high-lift cases in wind tunnels. Overall, a significant reduction in drag, improvement in the stall mechanism and accuracy in capturing the chine effect is seen with the addition of the wind tunnel geometry. The results invariably highlight the sensitivity of a multi-element high-lift system to the geometric details on and around the model and the ability of the code to accurately capture it.@en