Interesting I would have though that until the EKF shows white it would not have allowed you to arm i.e part of the pre-flight checks. Sometimes the GPS can't get a fix from a sufficient number of satellites when indoors but that should also have also stopped you from arming unless you have the arming checks disabled.
Maybe EKF is not part of those checks. I'll have to look into that further. Anyway glad that its working now.