That actually is the way it should be working, although there are a few issues with the client that seem to interfere at times. I notice, for example, that if click on the Sets button to display equipment sets rather than the character paperdoll, comparison popups don't work. I have also seen the popups fail occasionally with no obvious reason why.
As long as you have tooltips enabled in your client settings, you should see the comparison popups. It does work that way for me.
As a general note, ProfitUI CE is basically the same interface as ProfitUI Maintained, Reborn, etc. The big change was the development of a new updater and the creation of a new update host.
ProfitUI CE is the official version now, but I don't have any magic powers to clean out old versions that have been uploaded in the past.
-= Therendil =-