I have had the same issue with wall total R-value not matching the R-value that I've calculated manually. The solution I found was to: Go to the wall type Edit Type, select Edit box on the Structure row. In the Edit Assembly box, click on the material properties that you want to edit, and the box with the three dots. The Material Browser pops up. For this example, select Mineral Wool Insulation, and then at the top right, select the Thermal tab. The Thermal Conductivity is the U-value, which is the inverse of the R-value expressed as btu/(hr.ft.degree F). I usually think of R-value per inch as that is what the product data sheets for materials in the US publish, but notice, this is per foot thickness. For example, mineral wool has an R-value of 4.2 per inch thickness = R-value of 50.4 per foot. Calculate the Thermal Conductivity as 1/50.4=0.0198 btu/(hr.ft.F). Enter 0.0198 as the Thermal Conductivity for mineral wool.
Check the R-value for each material in your wall and roof assemblies to get the proper R-value to show up in the wall type Edit Assembly box, top left at Resistance (R). Double check to be sure each of your assemblies are referencing the updated material properties.
Another complexity I've run into is to have too many layers in the assembly. Either Energy Plus or Insight has a limitation of possibly 10 layers. I was modelling double stud walls with insulation between the framed walls. I got multiple errors based on assembly complexity. Since then, I've reduced the model complexity by showing a 7" studs rather than two walls of 3 1/2" and by removing incidental materials. Those complexity errors have stopped.
Please let me know if you see an errors in the above or know of a better way.
Thanks,
Richard