In my case, I discovered there were some hidden files. After getting rid of them, everything went back to normal. In fact, it started as a suspicion, because all the "regular" files were uploaded, so I suspected that something else should be interfering with iCloud. I prefer to use the Terminal in such cases, so I 'cd' to the folder and there they were: two temporary hidden files left by MS Excel. I couldn't delete them using the regular "rm" command, thus I decided to go around it - I copied the files that mattered to a temporary folder, removed the folder that won't upload to iCloud (with all the hidden file on it) and then recreated it and moved the files back. Now my folder's sync'ed and no more "Waiting to Upload".