Oh if only my paper flags would come out too dark. I have the opposite problem -- my inkjet printer colors are too bright.
I decided finally the printed flag was just a painting template. I give it a wash of thinned white glue to seal and stiffen it, then let dry. Then I overpaint it with relatively thicker paint, stopping and letting dry whenever it feels like the paint is softening the glue.
If it's not obvious, it's easiest to do most or all of this on the sheet before cutting the flag out. When done, seal again, cut out. Paint the white edges black or dark brown or whatever color is most appropriate. (Don't use permanent marker to do this; it works fine but if you ever do a superglue repair on it later, the superglue makes the ink run.) Once on the pole, if it isn't wavy enough, soften with thinned white glue, shape, let dry. Repeat if needed.
(With my print colors too bright, I have to overpaint every bit with a basecoat then highlight over it. If my colors were too dark, I could experiment with just putting highlight over the inkjet color.)
Yes it seems frustrating to go to all the trouble to print flags and then still have to paint them. But the plus is they have more of a handpainted look, and since it's the same paints used on your miniatures, the flag looks more like it goes with the finished figure.
An alternate method when you have too much detail for the above is to print the flag in black and white, then paint with stains (paint thinned to translucency) so the pattern shows through. Inks are ideal for this, except often their colors are too pure. But you can dull that down by weathering the flag with brown or black wash. Seal in between each step of course.
