It's not so surprising that the internal soundcard would have a low latency. Being closer to the CPU and sitting on a more responsive bus than the firewire interface, it probably needs less internal buffering to guarantee a steady flow of audio.
Normally you buy an audio interface for more reasons than simply to outperform the built-in soundcard in latency; better converters, multiple inputs and outputs, other audio formats, different clock rates, etc. If the FA-66 doesn't offer anything more than the built-in sound card, then I'd agree that you screwed the pooch.
-synthoid