How can the body become accustomed to allergy meds before the allergy itself?

Probably not true: The concept being asked to called "tachyphylaxis" where by repeated use of a medicine results in the med being less and less useful. This has never been clearly demonstrated for allergy meds. Probably what is happening when an allergy med is "not working" is that it is the wrong med for the symptoms or patient is develop more symptoms that require different treatment.