Randy,
You would need to chop those up into individual PNG's then you could convert them using the video coder.
Each PNG needs to be consecutively numbered, e.g. Image0001.png, Image0002.png etc..
James, it was probably an issue with Straight versus Premultiplied Alpha's. (Also known as Unshaped or Shaped). There is a setting in the video material to switch between the two modes. If you have it is not set to match the graphic then you will see issues with feathered edges..
#XPression