You can work around the changing gates glich by opening the .pln file in a text editor and manually entering a gate there. There’s a detailed post about this somewhere on this forum, try the search or Google.
I mostly do 45 to 90 minute flights and see this glitch on maybe one flight in ten.
edit: this is the post I was referring to: SimBrief flightplans change when selecting cold & dark start at a gate - #7 by IForkboy2I