I was experiencing the same problem and I can verify that this is the solution that works for me. Thanks. :-)
Note: it would be nice if there could be some kind of in-game note, explaining this. Personally I did not want to have the community overlay enabled in Steam games and my guess is that others feel the same. A simple notice would help solve the problem of not being able to add empire points.
Can you please verify whether the Steam overlay is enabled? If in game, you should be able to press Shift+Tab to view it. You can also check in the Steam client (Steam menu, Settings, In-game, Enable Steam Community in-game).