OK, here's how I like to think of it:
Story Ennis is far better at verbal expression, and also less inhibited. I can't imagine Movie Ennis ever saying anything like "I never shoulda let you outa my sight" or "I musta wrang it out a hundred times" or "Li'l darlin."
But just because Movie Ennis rarely -- or never! -- puts his feelings into words doesn't mean he doesn't know what they are. Yes, he tries to deny and hide them from others. He's terrible at expressing them appropriately. And he is a complete failure at acting on them in a constructive way. But I think he recognizes his feelings for what they are, as evidenced by his breakdown in the alley, his moments of wistful longing during their four years' separation, his elation when he gets the postcard, his burst of affection when Jack shows up for the reunion, his "prayer of thanks" remark (that's about as close as he ever gets to expressing love in words, and even then he undercuts it with the harmonica crack), his happy smile whenever he sees Jack (even in the post-divorce scene!), his jealousy at the prospect of Jack seeing other men, his grief after he gets the news of Jack, etc. He's not a verbal guy, but to me his behavior clearly indicates that he knows all along how much he loves Jack.
What he realizes in the end is that he blew it -- he should have acted while he had the chance, overcome his fears, taken whatever risks were necessary in order to be with the love of his life. He realizes that love matters more than anything else (indicated by his question of Alma Jr.).
Another difference is that Story Ennis seems to reject Jack's offer out of purely practical fear of violent consequences. Movie Ennis also makes that excuse, but I think that his fear is mixed with more shame and reluctance to admit that he's gay. Story Ennis seems to accept that more matter-of-factly. He's less homophobic. I guess you could take this as a sign that he's more in touch with his feelings, but I think it's actually a matter of being more comfortable with categorizing those feelings in a way that Movie Ennis couldn't allow himself to do. Until the end.