This article is from the Canine Epilepsy FAQ, by Alicia Wiersma-Aylward with numerous contributions by others.
There are many reasons why medical treatments can fail. The biggest
reason is the owner's lack of proper administration of the prescribed
drug. The progression of an underlying disease (such as brain tumor)
may resist treatment. Also, gastrointestinal disorders can affect drug
absorption, and tranquilizers may stimulate seizures. Drug
interactions can occur and adversely affect the level of
anticonvulsant drug in the dog's system. And it just might be that a
particular drug may not work for that animal. (LeCouteur).