That blinking might indeed be from his epilepsy, but the pauses I think are deliberate. When you have a petit mal seizure you do more than pause between words, you total blink out and even if it's just for a second you're like...UH....wha...huh? lol And during guitar solos it would be disastrous! I think Lindsey is lucky enough to have that problem under control.
But you know, I never even really noticed him blinking all that much! lol I guess I'm not very observant. But like Les said, that could very well be epilepsy-related.