I have been having this issue for some time now and its driving me mad.
I know I can get around it by using Ctrl-shift-v for pasting but I normally forget.
I even did a complete uninstall of my Atom app and reinstalled it and the result is the same.
Here is the video of the problem: http://www.youtube.com/watch?v=RuK7Zw08v0g
Thanks in advance for any help