Good day, when I upload any SimBrief flight plan (MSFS2020) and try to start from the gate, the route (waypoints) mess up (change), but if I try starting from the runway (as it is in the flight plan) it will be completely fine, so I have to start from the runway if I want to keep the plan as I want.
This is a known problem. If you import a flightplan from a file and then make any kind of modification to it in the world map such as changing the starting position or any of the procedures, the whole route is re-calculated using the planner built into the simulator. Unfortunately, this is not something we can prevent.
However, there have been a few workarounds! Please see this thread for a potential solution: