title: Anaconda and Spyder won't open if PythonPath is set
body: <p>I'm new to using Anaconda and Spyder and this must be a simple setting issue, but it's really frustrating. I need to have a PythonPath environment set because I frequently run scripts in ArcGIS which won't work without a path. However, neither Anaconda Navigator nor Spyder will not open if there is a PythonPath set. I get the splash screen, but that's it, it doesn't open. If I remove the PythonPath and reboot, Anaconda and Spyder work, but not ArcGIS. This is not an ArcGIS problem, rather Anaconda and Spyder just don't seem to like there being a PythonPath at all. Anyone have experience with this?</p>
  
  <p>For reference, my PythonPath contains:</p>
  
  <pre><code>C:\Python27;
  C:\Python27\Lib;
  C:\Python27\Lib\site-packages;
  C:\Python27\DLLs;
  C:\Python27\Lib\lib-tk;
  C:\Python27\scripts;
  C:\Python27\ArcGIS10.3\Lib;
  C:\Python27\ArcGIS10.3\Lib\lib-tk;
  C:\Python27\ArcGIS10.3\Lib\site-packages;
  C:\Program Files (x86)\ArcGIS\Desktop10.3\arcpy;
  C:\Program Files (x86)\ArcGIS\Desktop10.3\bin
  </code></pre>
  
  <p>I can remove everything except the bottom five and ArcGIS scripts still work, but it doesn't fix the problem with Spyder. It probably has something to do with the files not actually being executables, but links to scripts. For example, the shortcut for Spyder points to: </p>
  
  <blockquote>
    <p>C:\ProgramData\Anaconda2\pythonw.exe C:\ProgramData\Anaconda2\cwp.py
    C:\ProgramData\Anaconda2 "C:/ProgramData/Anaconda2/pythonw.exe"
    "C:/ProgramData/Anaconda2/Scripts/spyder-script.py"</p>
  </blockquote>
  
  <p>which seems to leave a lot of room for trouble. Interestingly, if I run from the Command Prompt, the first time there are no errors but nothing happens, and the second time it displays: </p>
  
  <blockquote>
    <p>Spyder is already running. If you want to open a new instance, please
    pass to it the --new-instance option</p>
  </blockquote>