I have observed a curious behaviour in 10.3 as well as 10.4.1. It's not a show stopper but does require me to close down ArcMap and restart it. I now have a brand new PC and 10.4.1 is a clean install on a new operating system (so no previous profile settings upsetting things).
After using ArcMap for a while any geoprocessing tool that takes a FeatureLayer as input (so you have your drop down listing valid layers you can choose from the TOC) looses the ability to select layers from the TOC. You are offered only the ability to select a FeatureClass.
Clearly if your processing relies on a FeatureLayer with a selection the tool suddenly becomes unusable! I find I have to close ArcMap and restart it. All tools behave as expected then eventually they loose the ability to offer up FeatureLayers again.
This can be frustrating and I am surprised to see this behaviour in the very latest 10.4.1. Are other people observing this behaviour?