How is it an outlandish claim that one of their system's crashed? Is it unusual that a computer system crashes even if it's a rare event?
If a website went down and the company said "the system crashed" you wouldn't believe them without proof? What could the FAA provide you to prove this?
Either it's extremely unusual (once in 21+ years), or happens more often than that but only this time did they decide to ground all planes in response to the glitch. In the latter case, then they must not be telling the whole truth, because they're omitting whatever is "different" about this time that changed their response to a glitch in this system.
