Apple do sell some of their videos with
Digital Rights Management (DRM), some without. This policy differs from country to country. E.g. in
Germany they usually sell music videos without DRM, but movies and tv
shows are DRM protected. Depending on where you live some of your
purchased videos might be DRM protected. You can check this in iTunes by
inspecting the "Kind" property on a video. If it reads something like
"Protected video file", Joobik Player
will not be able to play it.
Please check all of the videos not appearing in Joobik Player for the
"Kind" property in iTunes. If all of them are protected, Joobik Player hides them. This is a restriction by Apple. They let only their own apps access DRM protected content.
If you find any unprotected video not appearing in Joobik Player, this
blog post might help.