If I remember right, there was lots of funkiness with Windows 8 over the last year when it was in RC testing over at the site that supports that 3rd party tool which shall not be named here. Not sure if they ever managed to find workarounds for the wonkiness.

It's likely an issue (AGAIN) with how Microsoft is managing DirectX (which FFXI uses some very outdated implementations, which leads to a host of problems for GPU's released post 2010 in Vista or later Windows). Some of the more common tweaks that have fixed a lot of issues in the past: disable advanced features for the graphics card and/or game. For examples: turn off Catalyst AI (ATI specific), disable Dual-GPU support (Xfire or SLI), turn off shadows, weather effects, etc. in game...and so and so and so forth.

In short, FFXI simply isn't <officially> supported on the Win8 platform yet, nor the more recent graphics processors..