Phantom II Reinforcement Ability Reducing Cooldowns on Both Capital Ships

Phantom II just reduces the cooldwon for the reinforcement call of your capital ship, not for every single special. 

Then it is clear, that both chimaeras have still the same cooldowns. Perhaps you are fighting mirror matches concerning capital ship speeds and you are ending up in the RNG space for the ultimates. Perhaps a Reaper is involved? For clarification you should provide more information of the lineups, if the first sentence is not the answer for your problem.