I finally figured out a solution to this! It's annoying to do, but if you compress (zip) the folders/files that are stuck, it seems to kick the icloud upload into activation. You have to start at the lowest level of the folder that's in limbo, so for example: if Master Folder contains Subfolder, compress Subfolder and delete the expanded folder. iCloud should start to actively upload the compressed folder. Once completed, you can expand the zipped folder again, it will upload, and you can delete the compressed version. Then repeat the process for Master Folder. The deeper your folder structure goes for the files that are stuck, the longer this process takes, but at least it gets that "waiting to upload" notification to go away!