So I'm reading that you uninstalled and reinstalled both Indigo RT and the plugin, but the order is important.
In an old post from Peter (RL) I found the steps:
1. Install Indigo Plugin (with iClone 6 closed)
>>>Enter Indigo Plugin serial
>>>Enter Indigo RT For iClone activation code.
2. Install Indigo RT For iClone (no serial number required).
If you did it in this order and still have no luck, you may need to contact support at: http://www.reallusion.com/CustomerSupport/UserEx/QForm.aspx.
Note that it's the Chines New Year celebration, so they will not be back till February 1. But I hope there's no need and the procedure works.
Sometimes also, it's good to reboot after you uninstalled to start afresh.