That's because you're balancing the treatment in two different ways. Asthma meds usually work on a direct basis inside the lung to reduce the inflammation and muscle spasming that's already in progress -- taking these drugs prophylactically (for prevention) often means that asthmatic exacerbations are fewer and farther between.
But the inflammatory process started by an allergic reaction can be enough to overwhelm the control given by these drugs -- sort of like a reinforced door. It might keep most things out but if the pounding is strong enough, the door will still break down.
You might find that when taking the two drugs in conjunction with each other you're able to lower your doses of each. This is another reason why they recommend this -- because the drugs working together (something called a synergistic effect) often means you can take low enough doses to almost eliminate drug side-effects.
Have you tried Singulair? I understand it's sometimes helpful for people with allergies. It's expensive, though.
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