Re fire suppression system being involved in this problem, the systems I've seen are all designed so that a failure, loss of power, blown fuse, etc. will shut down the engine, not prevent a shut down. The fire system needs to be functional to enable the engine, otherwise it's disabled. Now I'm sure there are some corner cases where this might not be true, but I think you are much more likely looking at a stop solenoid or wiring issue.
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