I've seen this on another forum so I'll just copy the information from there to here:
Step 1: Go to your Run command, type REGEDIT and click OK.
Step 2: Go to HKEY_LOCAL_MACHINE, then click on Software.
Step 3: Click PlayOnlineUS and Square Enix folder, then the FinalFantasyXI tab.
Step 4: You should see 2 "strings", 003 and 004. Double click to open them, and change the value on 003 to 800, then change 004 to 800. You will notice the values to the right after you click OK will change to the corresponding resolution.
2048 x 2048 = 800 and 800
1600 x 1600 = 640 and 640
1280 x 1280 = 500 and 500