is your FFXI Config still not loading properly? There is more than just the resolutions that need to be set properly. There may be more issues bound to the registry keys than just 001-004 values. If FFXI Config is still knackered up, then there may be something missing, corrupt, or not registered properly at the system level. Hate to say it, but I've heard horror stories of people actually having to go back to an OS install to resolve some issues. Could try grabbing everything you can via Windows Update I guess to see if that fixes any potential issues like maybe a RAMDAC or VB or something bizarre like that.
Yeah it's still messed up. I honestly don't know what could possibly be causing this due to the fact that I've had the problem since the initial install, well before I messed with any settings. I could try a factory restore type deal but I feel like it might be just a hassle and not solve this issue.