I may have your solution, as I was having a similar problem when using the device to stream to my XBox360. The first few movies showed and played fine, but then none of the newly added movies showed up. Then, all the movies disappeared. I found the solution though.
You need to go back into the web interface administrative page. Do this by going to the device's IP address on your local network within your internet browser. In my case, it's 192.168.11.199, however, that is not typically what it would be for you, as my buffalo gigabit router gives it the 192.168.11.### designation and most routers use 192.168.1.### or 192.168.0.###. Also, I gave mine a static final number of 199, so I could always find it and never have any IP conflicts. Anyway, this all may be basic to you, but if not, let me know and I can help you out.
Once you've logged into the device, click the "Advanced" tab at the top. In the list on the far left, choose the "UPnP AV Server". It should now show a page allowing you to "Refresh". It turns out, after you add more media, you must do this if you plan to stream it (This applies to all media, including the iTunes server, but ONLY if you stream it). If you are simply using it as a storage device, copying or moving files to and from it, then the files will always show up, no need to refresh. You just can't stream them until you've told the device you've added new media through this step.
After I did this, everything showed up and played perfectly. One thing to note, though... At least with the XBox360, I couldn't play any media until the refresh was complete or I'd just get an error saying the device was disconnected. Depending on how many terabytes you've got in it, and how much media it's holding, the process may take some time. Be prepared for a long wait.
Let me know if that helps!