AI Flow and AI Ground should be a good solution to your problem one that will help overall performance.
These are two small freeware apps that will work alongside FSLTL to enforce better ground behaviour and separation in the air. They will stop the stacking you have seen and also greatly reduce the number of ‘traffic alerts’ that jam up the freqs when flying with a fair amount of FSLTL injected traffic.
Pick them up on flightsim.to