It's too funny. I'm exactly in the same boat. Spent two frustrating hours trying to figure out what I was doing wrong.
I got the 1st gen clear plastic flirc last year or maybe the year before but never got around to using it for some reason.
Last night I ordered two more (the new version) from Amazon.ca as I have three devices and thought let me program the old one while I wait.
I don't know what is wrong. The software does recognize it and like the OP, I updated the firmware but nothing I do lets me program the keys using the gui.
I don't suppose there is a way for me to exchange the old one for the new version? (I am in Canada BTW)