Yeah, I extolled the virtues of the Eye-fi card in a post a few months back -- I absolutely love it. The tech is marvelous, and they've done a good job sneaking a lot of functionality into such a limited space.
I do have some issues with the platform and the software. The limit of one one "local" and one "remote" destination for the photos is a bit of a drag, and has led to people using services like Pixelpipe to send them to multiple destinations.
I'm also not happy with how they implemented the FTP upload capability -- sending it to a server at Eye-fi which then FTPs to the server instead of just sending it to the FTP directly. Some forum posts by the developers/founders suggest they had some technical reasons for doing so (something about not wanting to waste space dealing with different FTP server types, passive FTP, etc.) but it's still a bummer, because if I'm at home uploading some HD movies, it can take a really long time (even on my fast fiber connection) for them to travel all the way out to a remote server and then back to my FTP on my LAN, when if it was just connecting to the FTP directly, it would be a lot faster.
I looked into that 3rd party software you linked to, but got distracted, and never got around to trying it out. Are you pretty happy with it? If I remember right, it only works when your camera's on the same network as the server? Can you still use it remotely the normal Eye-fi way through their servers?