Or perhaps Ennis was not savvy enough to realize that he was in love until much later...
Actually Ennis tells Jack at the reunion, I believe, that he finally realized it wasn't a bad meal that had him doubled up by the side of the road (in the alley, film) after they parted, but that it was missing Jack that did it to him. "That summer," Ennis said, "When we split up after we got paid out I had gut cramps so bad I pulled over and tried to puke, thought I ate something bad in that place in Dubois. Took me about a year to figure out it was I shouldn't a let you outta my sights. Too late then by a long while."
Of course, I really don't think he knew that his desire for Jack, as strong and as singular as it was, was love until Cassie told him what love was in the terminal.