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The OpenStudio SketchUp plug-in is sensitive to windows sharing an entire edge (or corner) with their base surface because SketchUp divides this into two faces instead of one face with an inner loop. However, this is just on the input side and it sounds like you are not having an issues there. This might be an EnergyPlus issue, OpenStudio and EnergyPlus do not share geometry processing routines so it is possible that EnergyPlus has an issue with windows on slanted surfaces. I'm not aware of any issues currently and I'm not sure what the implications on simulation results would be, someone from the EnergyPlus team should chime in here.