wow... been away for a while... surprised this is still going on. A few thoughts:
Just out of curiosity, when you reinstalled did you make sure you did a clean wipe of all FFXI files, folders, and registry keys to make sure you didn't have any mismatches? Also, make sure you are loading the Vista/Win7 compliant POL when loading from the ISO you downloaded. Think it's only included in collections released after 2008, forget exactly.
IDK if the FFXI Config uses it, but have you made sure your .NET is up to date as well (more people are using this framework these days, who knows if SE is on the bandwagon yet--could explain your screwy issues with the FFXI Config).
When you re-installed the DirectX to test for the missing DX9 files, did you use the web-installer, or the offline full distribution package. This is an important point. The web-installers tend to skip files once it detects a newer version of DX present. The offline install typically just copies them over regardless. This package was roughly a 100MB download if I remember right.
You mentioned earlier you switched back to Intel Graphics. If your system has both, one needs to be disabled or FFXI WILL have issues with D3D. This is a documented issue with the nVidia/Intel setups where people had to disable the nVidia and run on Intel. Think nVidia put out a beta last year that worked around it somehow, but the performance was still shotty either way on them. So, you may have to force it to run on Intel only by disabling ATI until a driver fix comes out if this is the same issue. If you are disabling the Intel and running on the ATI, the newest drivers may not be the ones to use. FFXI is notorious for having issues with the latest and greatest hardware and drivers. It's basically linked to the shift to DX10/11 compliance (DX9 and older is run in emulation at the Windows level, causes all kinds of wonkiness). On the newer hardware, older drivers often have to be used.