I just discovered something really annoying, and that is you can't have manual supports on just one model on the build plate.
Assume you have manually added the supports you want on one of the models. Support generation must be turned on in the profile, and for this one model everything works as expected. However, for the other models that you don't really want support on, S3D will then auto-generate support material.
This is annoying as hell, and the only workaround I have found, is to manually add some support material to all of the models, even those that shouldn't really have any.