Did you create them as pads, or did you draw them with the drawing tool? I've never seen anything like that. Post your files.
i drew them free hand because the pad tool doesn't let you use more than one pad size. (when you go to change the pad size it changes the sizes of the pads i have already made)
You can't do that. There's no way to change them into pads after drawing them, even though you CAN change them to a copper layer (TOP, for example). It simple won't treat them as a pad.
So let me explain how it works because it's confusing. The pattern itself has pad properties...size, shape, type, etc. This is convenient because 99% of the time, all of the pads are identical, and when you change the pattern's properties, they all change. What I would do is make the small pads use the pattern's pad properties, and then for the larger pads, uncheck that box bookaboo mentioned, and you'll be able to change them.