Not to disparage the JSF too much, but they are just being careful. It's almost certainly not a software issue they are concerned about but a fundamental issue with the design. Due to trying to cut the weight down, the fuel now also doubles up as hydraulic fluid in certain sections of the airframe. I'll leave you to figure out if that is a smart idea in a combat aircraft. They are currently still working on finding a reliable back up system to put out any flames after a lightning strike or combat damage - hence no storm flying. Unlike other aircraft hit by a lightning, there is a very good chance the JSF would explode in a rather large fireball as the main fuel tank goes up, and that is rather embarrassing on the way to an airshow! Like most technical hiccups they will get that little glitch sorted eventually. Throw enough money at a problem and you can solve most things.
