Make Windower use Registry settings instead.

I have no idea why this happens.
Just got Windower and its really amazing, but no matter what res setting the mouse is always way off from the in-game mouse.
Even with Hardware Mouse On/Off
So I deleted all lines relating to resolution in hopes it would just use the ones from Registry that I already modified till now.

  <profile name="0001">
    <consolekey>Insert</consolekey>
    <windowmode>Window</windowmode>
    <uiscale>1</uiscale>
    <supersampling>2</supersampling>
    <bumpmapping>true</bumpmapping>
  </profile>
</settings> 

Everything works perfectly when I run FFXI without Windower, but when I run FFXI through Windower, the mouse is off, resolutions of overlays, menus and background is all fixed at 1920x1080 which I dont want.
How can I make Windower use my current registry settings instead of its own.
I want Windower for the add-ons/plugins but not for its "window"er features. =)

If the settings are not in the settings file then Windower defaults to using your desktop resolution, so don't remove those lines. Make sure that you set the resolution on the profile edit screen. If you want to increase the background resolution to get fake FSAA, then enable super sampling on the "Game" tab. If you want to increase the size of the menus then increase the UI scale setting with the slider.

The hardware mouse will only work correctly if UI scale is set to 1, and you play with a borderless window. The software mouse should work just fine with any setting. These limitations will not be fixed in Windower 4, but are already fixed in Windower 5 (which, unfortunately does not have a released date at this time).

Ah thats why.

Theres no way to just use the addons and plugins feature of Windower -- Only?

I want to use windower but I cant even play properly.

You can use fullscreen mode if you wish, this essentially disables the "windower" portions of Windower, but you will lose the ability to Alt+Tab. There is no way to use SE's official windowed mode with Windower. If you are OK with using the software mouse then you can just set everything up the way you used to have it within Windower, if you want to use the hardware mouse then you will need to stay within the limitations I mentioned previously.