Then it's not picking up the media in it's scans.
Make sure that the directories in question are actually included in the Plex sections and that all the expected naming conventions have been followed. The other thing you can get rarely is if it has detected the new thing as something it already has it'll merge the entries together.
You can run manual command line scans in Plex as well (this is on OSX so YMMV on Ubuntu so experiment) by firstly running the Plex scanner executable with a --list option to get a list of section numbers and then running it again with --scan --deep --refresh --section X where X is the section number from the first command.
You might want to touch the things which you are scanning for first so it looks for changes when the scanning runs as the file and directory time stamps have changed (do the touch on the directory as well as the files).