What file (TGA, BMP etc.) and how many colors is the final image?
The colordepth does matter mostly I think.
And it sure helps to use layers instead of drawing it all in one layer.
You can adjust things much more easy afterward or even remove them wher it doesn't work as you want.
I paint every color in the camouflage scheme on a seperate layer. I have several layers for dir, dust and weathering. Then I have several layers to create a bit of highlights and shading.