I'm not sure what you mean by the "Alphafold Run window is dark".  If no structure appears in ChimeraX than the prediction did not complete and that window shows the error message.

  For your second run where you sent an image of the error message, the error means you tried to run AlphaFold prediction in ChimeraX 1.3 or earlier (which does not handle complexes), then you soon after tried to run ChimeraX 1.4 daily build AlphaFold prediction which uses a newer AlphaFold version.  The second run saw that AlphaFold was already installed on the Google Colab server by your first run with ChimeraX 1.3, but it was an older AlphaFold version that will not work with ChimeraX 1.4.  You would need to reset your Google Colab runtime to get rid of that old AlphaFold or wait several hours and Google Colab will terminate your session getting rid of the old AlphaFold.  I should have ChimeraX 1.4 check to make sure the AlphaFold that is installed is new enough and warn about this rare error.

Tom