This is an issue with the old FT3 that is fixed in the newer FT 3.5.

The issue is that FT3 saves its settings in the program directory, which windows only allows if you run the program as administrator (Right click the shortcut -> Run as administrator)

By default, templates only contain references to the fills used for the style (You REALLY don't want to have them all listed, trust me :)), so that means that drawing tools not made for the current map style will show up using the currently selected fill (see your status bar), instead of the actual fill used by that tool in it's native environment. (Your current map seems to be the Ancient Tombs style)

There's more information in this FAQ topic, including how to import the fills to the current template:

Sorry to hear you have so much troubles, but hopefully you'll manage to sort it out.

When you say wiped 40% of your map, make sure to check out things like sheets and sheet order. You may end up with something on an unexpected sheet after ungrouping, which means things may just be hiding out under something, like below instead of above your landmass or other terrain.

Not for lines. Polygons gets a hollow middle whenever the line width is greater than 0, but lines will be solid all the way, unless you use the "hollow" fill style (You're not, since your rivers are using a bitmap fill) OR you have an Edge, fade inner effect on the rivers, where the inner opacity is set to be lower than the outer one.

Looking at your drawing, you do have an edge fade inner which is way wider than your rivers which is also the partial cause of your rivers being very difficult to see. I didn't notice that immediately when I looked at the map earlier because I worked with effects off to see it without the glow. You can try changing the width of this effect to something like 0.2 and see if that works for you.

For that map, line widths less than 1 seem to be a bit to small to be visible, especially when zoomed all the way out. Using effects like that is a fine way to make lines more visible, or you could bump the line size a bit. I am guessing that doubling the size of the rivers should be fine.