My Harmony still controls Hulu just fine through the Logitech adapter, which shows up as #7 just like the Sony PS3 Remote. Try running the sync routine again, so that the PS3 and Remote shake hands and reintroduce themselves.
Also, you should never expect CEC to work, but instead should just be thankful when it happens to do anything at all. As with many of the "standards" in this retarded industry, it has become so polluted with proprietary crap as to be pretty useless most of the time. If you just bought a new TV, then it probably broke CEC in your setup.