When using FINAL FANTASY XI via Steam, one should install everything related via Steam, and only Steam.

So uninstall everything related to the game, even the PlayOnline Viewer (I would move or rename the old FINAL FANTASY XI folder(s) if you have done major updating on them as you might be able to skip updating by replacing the newly installed files with the updated ones), then do a clean install via Steam, or which ever medium you wish to use.
That being said, you can use any other medium just as well, and register any expansion packs or/and add-ons to your account with the registration code from Steam.

You do not have to install via Steam to use the registration codes from Steam.
(In case it has been, or will be changed at any time in the future, I will say that it used to be like so.)

Personally I would not recommend using Steam at all, if possible, for various reasons.
But that's another story, really. ^^;


For now, I think that is all I have for you.
Obviously it is not an official response, so take it for what it is.

If you still do experience problems, please include what you have tried so far to let us better narrow down our suggestions.

Good luck!