Windower crashes because vanilla FFXI tries to return to POL in an unusual way. Your only solution currently is virtual GFX (like DgVoodoo). Square Enix has previously stated that they don't consider this an issue.
Isn't this a dx8 issue? or rather "functioning as designed" as the game was designed to crash when losing fullscreen so people wouldn't alt+tab in general and they never "fixed" it even when making a windowed option.
As to the OP: anything that causes you to lose directx fullscreen (unplugging a monitor, UAC, ctrl+alt+del in not ancient windows will all cause it, as said above dgvoodoo is a workaround, just don't put the settings too high or you'll randomly crash your video card driver.
Other options: don't unplug hdmi cable, don't lock pc, don't use ctrl+alt+del (ctrl+shift+esc can bring up task manager directly), put UAC on 2nd lowest setting or lowest (off, some don't recommend).