Thanks for the update.
We have encountered this as well, and changing the resolution seems to fix it. Maybe you quit Eye-Fi Center while the other screen was still connected. Our software remembers its last screen position and tries to return there when you launch it later.
I think if you disconnect the screen while the program is still running, the Mac will return all your apps to the main screen, including Eye-Fi Center, so that might work in the future.
I'm not sure if this is something we can fix - it might be a quirk of the Titanium platform used to build Eye-Fi Center - but we've reported the issue internally.