Question
My mother had a tree struck by lightning twice within a week. The irrigation control box on outside wall near the tree flew off wall and burned. Power in her home went out. Licensed electrician said the system GFCI receptacle was improperly wired--hot wire loose outside and ground wire connected to hot wire in the indoor receptacle. Irrigation company is saying not their fault and that their system should not use GFCI or be grounded anyway. I am suspicious and need to know the facts from an impartial expert. Thanks!

Answer
Interesting situation.
The controller shouldn't matter whether it's on a GFI or not. Irrigation controllers routinely aren't grounded unless they are part of a large system. (golf courses) I'm not clear as to who wired the GFI, an electrician or the irrigation contractor. If the contractor just plugged into an existing GFI then I don't see them as the bad guys.
I can say reasonably certain. The controller would have blow-up whether it was on a GFI or not. Lightning strikes on or around a home usually gets the irrigation controllers. They have a wonderful grounding system with the wire which goes out to the valves. No grounding would have prevented a close strike from cooking the controller.
You home owners insurance should cover the lightning hit. Be sure whomever repairs the controller also check the valves. Often they too are burned if the controller gets hit.
Feel free to reply back if you have other questions.

Matt