I have the same problem and moved my Downloads folder from the home back onto the dock. The result is that the download folders now just looks like a default folder on the dock.
I noticed that it's changing its look based on the contents in the folder. If I remove all the files, the icon is the default download icon. If there are just zip files from my downloads, then I see files on my dock. If there is a folder within the downloads folder, the downloads folder will change to a folder with folders within.
But how can I get the default Downloads icon folder back onto the dock?
I hope I didn't make this confusing.
EDIT: nvm, I just needed to check the properties for the folder on the dock to see it as a folder and not a stack.