Joobik Player plays videos from playlists synced to your iPod, iPhone, or iPad. To use it, please create a video playlist in iTunes and then sync the list to your device, not only the videos themselves.
For example: To sync a movie playlist, on the tab where you select videos for synchronization in iTunes, you have to either uncheck the "Automatically include" checkbox, or with the checkbox checked you must choose any other option than "All movies" from the drop down list in order to display the playlists for syncing.
On the "TV-Shows" tab it is the same.
If you have a mixed playlists, containing movies and tv shows for example, this playlist must be selected under the "Movies" and the "TV Shows" tab for syncing. Otherwise it will only contain either of the video types when synced to your iOS device.
iTunes Match Users: If you are using iTunes Match to sync your videos to your iOS device, you must download the videos from iCloud to the device in the first place. Only then they will appear in Joobik Player. Downloading can be done with the standard Apple iOS Video or Music App.
When iTunes Match is turned on on your iOS device, Joobik Player will not be able to recognize iTunes Folders.
Detailed instructions about iTunes Match can be found in this blog post.