That certainly does make sense, about the pixels being offset, but animation is Literally scrolling up. The cubes are all running the animation correctly, and each cube is actually moving up. Does that help clarify what I mean? If not I'll post a video.
No, I know exactly what you mean. Again, that's exactly what should happens when you have an offset pixel like you have. It's doing what you told it to do, even though that isn't what you want.
Don't believe me? Load your image into the image editor of your choice. Turn on the grid feature and set the width and height to 32 px. Then scroll down. Notice how each frame seems to be a little higher than the one above it in the grid square? That's exactly what you're seeing in Minecraft.
Nice tutorial but say I wanted to make it 64x64 instead of 16x16 with hmm 5 frames, how would I do so?
This is addressed in the tutorial. The process isn't any different. The only change is that each frame is 64 x 64 instead of 16x16. This doesn't change the number of frames, or anything else about the .mcmeta file.
Thanks for the guide. How do you animate paintings?
You cannot do this with vanilla Minecraft. You must use a mod like MCPatcher for that. This guide only covers vanilla animation method, however, so the only advice I can give to you is to look in the "Information for Texture Pack Authors" section of the MCPatcher thread, or to do a forum search for "Animated Paintings" since I know there have been several guides written on the subject.