Well, this is a bug that's been around ever since conveyors were introduced. It is much less pronounced now, but still there. So I think we should brainstorm as to why it occurs and ways to prevent it. So many quests use conveyors now that it really gets annoying when you're playing and suddenly Link becomes uncontrollable.
I seem to recall someone saying that it happens because Link gets off the movement grid. In this case he needs to be snapped back onto it whenever he changes direction. True, but that seems to already be attempted. Perhaps what is happening is Link tries to snap back to the grid, but the conveyor continues to act on him, pushing him past the grid and making him misaligned.
BTW, when I say Link snaps to the grid, I mean how he will move a little further to ensure his movement is on some 8x8 boundry. For instance, try moving Link a pixel or 2 to the right and then walk up. He'll move more to the right first until he's on the 8x8 boundry before moving upward.
Another option I think would be to leave Link misaligned while on the conveyors and only realign him when he leaves them. One benefit to this would be that his movement on the conveyors would be a lot easier to control. Unfortunately, this wouldn't alleviate the problem when Link leaves the conveyor, it would likely still misalign him. So the first solution would still have to be implemented to prevent that.
Anyone care to add to this?