Could this be perhaps caused by a dpi setting?(I've got it set so that everything is a lot smaller so that more things can be fit on the screen) Looking at my Skype layout it looks like it does on my Nexus 7 tablet. Maybe skype thinks that it's on a tablet, hence the proximity sensor is not being employed. I don't have a Speaker phone button either. This is just a theory, I'm not willing to test it by going to default Dpi as it screwes my entire layout, icons, folders etc.
Sent from my Nexus 5 using xda app-developers app