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"Legendary Flame Lord" gets Spell Counters when Spell Cards resolve, not when they are activated.
If you activate a Spell Card, and your opponent chains "Call of the Haunted" to Special Summon "Legendary Flame Lord", "Legendary Flame Lord" does not get a Spell Counter for that Spell Card because "Legendary Flame Lord" must be face-up on the field when the Spell Card is activated and when it resolves in order to get a Spell Counter.
You place a Spell Counter on this card when the Spell Card resolves, so if "Magic Jammer" is used to negate the Spell Card's activation then you do not place a Spell Counter on this monster. But if "Imperial Order" is chained to the Spell Card, you still place a Spell Counter on this monster because the activation of the Spell Card was not negated. If the Spell Card was a Continuous, Equip, or Field Spell Card, and “Dust Tornado” is chained to its activation and destroys it before it resolves you still place a Spell Counter because the activation of the card was not negated.