It's possible you haven't waited enough after the simulator closed to start it again. Yes, even if the P3D Icon has disappeared, depending how many add-ons you have loaded, how free memory you have, it might take a while even well *after* the icon has disappeared for the sim to be really safe to be reopened again.
If you want to have a feel how much you should wait on your system, open the GSX Control Panel when the simulator is running, and note how much it takes for the "Compile" button to become available after you close the simulator. That's when it's really safe to restart the sim again. Try the same test using this method.