1. Actually read the rotation. You can see it under /hekili > Action Lists.
2. You can enable Debug mode ( /hekili > General Settings > Debug ) and then use the Pause toggle (/hekili > Toggles > Pause ) to see why it is being recommended.
3. CL gets recommended very early to activate the Alpha Wolf trait.
4. The default action list in SimulationCraft (on which I base the defaults) moved FT/FB under Stormstrike in priority. My own simulation testing shows that this was a bad plan, and the next release will move those back up in terms of position.
For a temporary workaround, you can get this import string: http://pastebin.com/GKWh1PXt
It goes here: http://i.imgur.com/6WHJOie.png
That will move FB/FT above Stormstrike in priority. I also plan to move Doom Winds higher in the priority, but need to run sims to prove that it should be moved first.