Either your controller is faulty, or your fingers are just tired. I'm betting on the latter. I noticed that when I used to practice SHDL, my right thumb was worn from sliding between Y and B. It burned.
I've been playing with ATs for about a year now. My skills are finally (somewhat) second nature. Too bad I don't have any opponents. I can waveshine across the stage just fine. It's just waveshining backwards and waveshining in battle. I'm not amazingly consistent, but I'm noticing major improvement. Mainly though, I have trouble waveshining backwards (especially consistently). Well, that's my smash story. XP
It's just muscle memory and muscle endurance. I noticed yesterday that when I tried to wallshine my sister's Sheik, I would screw up after 2 shines. T-T After you play for a while, your hands are bound to be tired. Maybe your hands just get tired quickly? Well, the best advice I can give you is practice. Practice by yourself to get a better handle of the rhythm. Practice against a foe to learn to pull it out on the fly.