We are sorry to hear you are still having this problem. It is not one we have seen before. In the LightBlue Explorer app, are you judging the number of services by what it says in the "Peripherals Nearby" list? At that point, before you have connected to the Bean, it will always say "1 service", because that's all it sees from the advertising data. Once you connect to the Bean, it should pop up with the special Bean interface (including the rainbow LED control). From there, if you go to Options->Service View, you should be able to see all the services. If this is not the case, could you post a screenshot of that view? Could you also then go to the Log at the bottom right corner and post a screenshot of that view?
Also, if the Bean control view doesn't pop up at all, that is a separate problem, so let us know if that is the case.