more of what WildBill said:
When it comes to paint, did you use all of one brand? For example, if you used let's say ModelMaster for the dark green and Gunz for the light, these two brands wern't formulated to look "right" side by side. Some paint manufactuers shift their entire line lighter, some darker, or some toward a blue hue (just for an example). If you use all one brand, typically the contrast between these two colors will be acceptable.
Now adding a gloss coat is another ball game. The darkening affect you mentioned is typical but can be reversed with a dull coat. I typically use Future for gloss but an old inventory of Pactra Flat Acrylic for the final flat coat. I've been happy with those results. I just finished my 1/48 ProModeler Stuka that way and it turned out great (witht he Model Master paints underneith).
"I love modeling- it keeps me in the cool, dark, and damp basement where I belong"
Current Projects:
1/48th Hasegawa F-14D- 25%
1/48th Tamiya Spitfire- 25%