This has been happening to me the last few weeks. Every time this warning appears, and I believe that they are enabled, I verify, and yes they are enabled.
Just to be safe, I disable, then re-enable. The warning stops then.
And one time, to be very safe, I flew it towards some trees, and it triggered the system, indicating that it was in fact enabled.
But then it returns every time I change batteries.
I think it's just a bug.