My Lady is also an epileptic. She was diagnosed when I adopted her at age four so it's hard to know how long she'd been having seizures, but the normal age for idiopathic epilepsy to surface is between 1-5 years.
Has your vet checked Stewie's thyroid function? That isn't done during a routine CBC. Abnormal thyroid function can also cause seizures.
Lady is now twelve and proof that epileptics can live along, happy life. She has been on medication since I got her, but I am happy to say she hasn't had a seizure in over a year.
This website is the best source of information on canine epilepsy on the Web IMO. It's become my bible over the years.
http://www.canine-epilepsy-guardian-angels.com/