Also, if this happens only after a restart of the simulator, it might because you restarted the sim too quickly after closing a previous session, not giving it enough time to release all open files and file locks, so the next session cannot start, because the one from the previous one is still closing.
If your system is overloaded with too many addons, you are short on physical memory, if the system is swapping virtual memory and physical memory from the hard drive and, regardless how fast it is, even the fastest SSD is dozen of times slower than real memory, so it might take a while to clean everything after the sim has been closed.
The only solution, other than waiting a while to ensure everything has been closed (you can use the Task Manager, and wait for Couatl.exe to close, instead of waiting a random amount of time), is to either increase the RAM, or reduce the number of addons loaded or your settings.