Hi kblver,
The reason that Quicktime is opening on those particular videos is that we had to use a different encoder for them, which, depending on your settings will open with Quicktime rather than iTunes.
The easiest solution is, while iTunes is running, to drop the two movies into the main window of iTunes. This will import them into iTunes (which happens when it plays a video, anyway). You can then play them from your Movies within the program.
On the Mac, you can also select the video by highlighting it in the Finder, type command-I, then toward the center of the window under "Open with:", choose "iTunes" from the list instead of "Quicktime." If you click on "Change All..." it will enable iTunes to always open that type of file.
If you are on Windows, right click on the file and from the "Open with" submenu that pops up, choose "iTunes" from the list and iTunes will then open the video.