Ok, I think I figured this out, and I want to post this here in case it can help anyone else.
I have FFXI installed through Steam, and I have the steamapps portion of my Steam folder running on a different HDD, and linked with the Link Shell Extension. You can imagine how frustrating to look for anything to do with Links or Shells or Linkshells and FFXI. Entirely fruitless.
Note: There normally is no problem at all, but the SSD I have Steam installed on has less than 1GB of space, and so when I went to install FFXI updates, it wasn't letting me because the registry is pointing to the nearly full SSD.
So, the key is, to find the registry files, somewhere in or around:
HKEY_LOCAL_MACHINE\SOFTWARE\PlayOnlineUS if you have a US version,
HKEY_LOCAL_MACHINE\SOFTWARE\PlayOnlineEU if you have a EU version,
HKEY_LOCAL_MACHINE\SOFTWARE\PlayOnline if you have a JP version.
(If you are on a 64 bit machine, its HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\PlayOnline...)
and update the entries with the real path of the PlayOnline and FFXI folders.
Then, run pol.exe through the real PlayOnline folder, and not through steam. Boom, it works.
Just thought I'd share.