Sadly, the “beacon configuration wizard” bundled with the Indoor SDK currently depends on Estimote SDK pre-3.0. And beacons with firmware 3.0 require Estimote SDK 3.0 to be able to connect to them. Which means that at this point, it’s not possible to do automatic beacon configuration of beacons with firmware 3.0 via the Indoor SDK. You’ll need to configure your beacons manually (max broadcasting power, advertising interval 200 ms or less, basic power mode disabled) and then press “skip” on the auto-configuration screen.
We’re working on migrating the Indoor SDK to use Estimote SDK 3.0, but this will still take a week or two.
Note that the indoor positioning itself works just fine with Indoor SDK and beacons with firmware 3.0—it’s just the auto-configuration part.