As the program doesn't actually interface with FFXI in any way, I can't see how it applies. It's just capturing the bits that are rendering to the screen and saving to a file, not interferring in anyway.
On that note, MANY videos and screenies of the game have/are being taken with this app, none of the people that do it have been banned or warned yet (just look at ffxionline.com's video section, that's almost all fraps based). I'm always running it and have never had an issue.
Z