Unreal launching and packaging intermittent issues

Unreal launching and packaging has been hit and miss sometimes I need to delete the saved and intermediate directories, sometimes I have to reset my computer, sometimes I have to restart the editor and sometimes it just works fine and I can work on my game with out worries. I’ve had the issue since 4.7 and still now in 4.8.

Looking further into my issue: https://answers.unrealengine.com/questions/245155/i-can-launch-my-game-but-cant-package-it.html

It seems like this happens when I delete things and they don’t actually get removed from the content directory.

Is anyone else having this issue?