As far as in-house developed games go, Square Enix has always had a bad track record when it comes to MMO PC performance. They have made improvements in recent years, but only when using someone else's game engine: The Last Remnant (Unreal Engine 3 and Steamworks) and Gyromancer (Bejeweled Twist) both run quite well on PC.

Does your system hard drive have write caching enabled? If you don't want to splurge for an uninterruptable power supply, you might want to try turning write caching off and see if that helps with your problem.

I've seen many problems in the past with write caching-enabled hard drives that become heavily corrupted when an unexpected power outage occurs, which we usually attributed to cached data being lost before it could be written to the hard drive. Granted newer hard drives and operating systems are more dependable when it comes to write caching, I still don't trust it enough in ye ole generic workstation to enable it (especially when the performance boost is virtually unnoticable to Joe User on newer machines when running generic desktop applications).