under "Performance & Quality Settings" the "Global driver settings" were set with AA at 8xS Anisotropic filtering at 16x and Vsync On. (Image Settings were also set to HQ, but I didn't change that). I also checked and there was no profile for FFXI.
I created a profile for FFXI and browsed for pol.exe and polboot.exe, then making that profile Active (selecting it in the drop-down at the top of the window) I checked all the settings above and then set them to "Application-controlled".
After saving my changes I loaded FFXI and walked around the AH in Jeuno. There were many more people visible than before, my weird flicker issue was gone, and people didn't wink in and out of existence as I would spin the camera around. As far as I can tell, it worked.
Now, I didn't spend too much time tweaking this out... I may have turned off too many things (Vsinc should actually help reduce flicker). So you may want to play around with some of these and see what works best for you. I just wanted my problem fixed... and it seems to be for now.