OK, never ever use the on screen colours in the pattern as a guide! It's really hard to accurately reproduce the colours from the dye baths on screen, so mostly they just pick something that kinda looks ok! 

With KGChart and PCStitch, the pallettes they use to display on screen colours are pretty dissimilar. More so in recent versions of both programs, in my experience. They aren't and probably never will be the same as the thread, and the patterns look different on different monitors.
What you should do is compare the thread numbers - if possible you should check the colour from the original image against an actual thread in daylight. Do invest in a colour chart if you can do that (and don't have a full set of threads).
As to your thing with the dark blues - you can either brighten it and see what happens, or leave it as is and use something like a 939 for the blues (although sometimes that's hard to distinguish from black!)
If you still have trouble, ask for help! We'll do our best to sort you out with a pattern 
 
Hope that helps a bit!