As iFMRTE needs to access FM process memory, it needs to be executed with elevated privileges, so it asks you, if you authorize it to run as root or not.
If you answer 'No', iFMRTE will run as a normal user, but it won't be able to load the game data, as it cannot access it.
If you answer 'Yes' iFMRTE will run as with root privileges so it can read/write data on FM.
Now, about the loading issue, I'm installing OSX 10.9, so I can see if I can replicate this issue, as soon as I have more details, I'll let you know