In my case, it changes both the plan and the 3D view but the door/windows become distorted because their proportions don't match anymore.

Your problem might be related to a bug I reported with wrong deformations in the 3Dview with the Pan3DView plugin: http://www.sweethome3d.com/support/foru ... ,100#61531
One thing I figured out that might help you with finding the cause is to place an object horizontal and one diagonal and see the difference in how the deformations show. You will also have to check chained deformations (deformation on a deformed part).