Model will only work in Model Builder

I created a model that selects address points inside of a polygon, removes points points based on certain criteria, and creates a feature layer from the selection. I can get it to work from within Model Builder by clicking Model > Run Whole Model. But when I save it and run it normally, it doesn't create the feature layer. I've done it several times to be sure. I've exited out of ArcMap completely, and even recreated the model from scratch, and I get the same result. Has anyone seen this before?