"The system cannot find the path specified." When running script with Shebang

When I try to run a python script with a shebang like `#!/usr/bin/env python` I get the error `The system cannot find the path specified.` When I remove the shebang the script works as normal however. Is this a problem with Atom starting in the wrong directory? I tried starting it from the command line in root but that didn't fix it.

This is also likely a problem for most scripts (I believe this occurs when running Perl scripts as well).

Start by reproducing the failure in atom-script with a Python script using `#!/usr/bin/env python`, then compare it with the same script without the shebang. Check whether Perl and other shebang-based scripts show the same behavior; done means supported scripts run successfully without the path error.

Written by the indexing model from the issue text.