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Answers
I have the same problem on both Peppermint 5 and Windows; so it's not an OS specific issue. I guess it's time to file a bug report; but I only just started using Atom so not sure where to find any helpful debugging info :/
I also started using Atom more or less 2 weeks ago.
But only for the purpose of learning TypeScript!
For now, it's installed in Win8.1 and working alright.
I need to buy a simple cooler before returning to my Linux desktop box! :>
However, I started using SublimeText with Processing package, but recenty it was an update about package of Processing in Atom; now it works, but Atom open 2 sketchs (it is not a problem for me).