Hi Alex,
Thank you for sending the file. It looks like there are some shading values that SAM is storing from a previous run that are causing the problem. I'm working with the developers to resolve this, but as a workaround, please try this:
For each of the three cases (Metal Roof-E, Metal Roof-E, and Flat Roof), on the PV Subarrays page, click Edit Shading, and then click OK to close the shading window. After you do that for each case, you should be able to run simulations without generating the error. (Because the first two cases use the Multiple Subsystems option, you'll need to do that for each case before running simulations.)
Please let me know if that works, or if you have any other questions.
Best regards,
Paul.