That is why you would use Thrusters on ships with short range and not your missile boats. You want the missile boats hanging back and launching long range missiles while your kinetic weapon ships rush in to hold them off. I use thrusters, especially on my kinetic weapon ships and it definately helps if you utilize your ship roles and strategy for them.
I have the same issue on 3 of my 24 planets. They are all in areas close to other races with the borders influenced by other races, but dont think the influence goes all the way to the planet itself. Also, 2 of the 3 planets has ships from a somewhat unfriendly bordering race, although I am not at war with them. Still, one plant is bordering the Alterans with I think the same Ideology as me and I havent seen unfriendly ships in the area. I think there might be one bord
After doing some troubleshooting of my own this is what I have done and my "temporary fix" I had uninstalled and reinstall all the files (excluding the user file). When I did this the game worked fine, exiting to main menu and starting a new game, I did this about 10 times to check. Then to double check the "new" integrity, I ran that on steam again, and again it found 2 files with integrity issues and deleted them saying it would replace them with correct files.
I played the game with no problems with all dlc except the 1.3 patch, the snafu(?)(squirrels), and any steam workshop content. I've since had the game patched, downloaded the new race dlc (so now I have all DLC), and downloaded some (about 8) factions. I since have removed the workshop races to see if that would fix the problem and opted for several of my own created factions. So, now when I start a game on occasion I get every star with only "Dead" planets. Al