Solved. See below.
I'm fairly new to Python so please bear with me. Using atom and flake8 really appeals to me and a good way to point out my errors, and thus help me learn.
The irony of this situation is that I've been able to be get flake8 and hydrogen running on Ubuntu 17.04, but Windows (supposedly more user friendly) is killing me!
linter-flake8 always throws up a message about the PATH and CMD.exe. I think this is all fine, and Py2 and Py3 can both be called from anywhere in the CMD.
I know that atom says I can specify the location of something to fix this (sorry, working from human memory here), but despite hours of tinkering and looking I've had no success on Windows 10. Ubuntu was much easier by comparison (which is sort of counter intuitive). Maybe there is just more online help for Linux systems!
Can't anyone help?
I ended up fixing this with online help. I believe I ran into trouble because I had installed all packages within atom itself.
I may have have installed the pip packages incorrectly.
Anyway, I removed everything and rebooted. Then followed this:
Then, I made sure my environment variables were correct. I want Python 3 at the top.
Then I reinstalled Atom and updated. Rebooted again.
Then I installed everything through pip3 and apm on the command line, rather than through the UI in atom editor.
Started atom, allowed firewall, let it update dependencies.
Rebooted. Worked! Still not sure why though; what I've done this time is essentially no different as far as I can tell.