The stock OS, and the CFW are completely different. It's not surprising that apps for one will not work on the other. The CFW has better performance, but less content. The stock has a lot of additional software, but at the cost of performance. At this point it's a matter of choose which one suits your needs. There is a bounty currently active in hopes of getting one of these devices to Pingflood which would allow for a port of RetroFW 2. For the time being however, those are your options.