Sometimes I get a wad of paper stuck in the line. I can see it when I flush. No matter how long I hold the handle down the water just isn't enough to push the wad through. That's when I hold the handle half way as if doing a #2. I let the bowl fill almost completely up and then push the handle all the way down. That large flush of water usually pushes the wad of paper through.
Just something that might be happening to you.