I'd suggest updating your software, as that few layers is a big handicap.
There are various reasons why the "right" colours can look wrong on a skin:
First aircraft tended to be left outside in all weathers and paints were subject to colour shift as a result, some more than others. For example the red on Japanese markings faded to a reddish-orange over time. Some aircraft were kept a lot cleaner than others as well, a layer of dirt can make a big difference to the look of a skin.
When researching colours be wary, particularly of profiles and warbirds, even some colour matching websites can be suspect. USAAF planes used well documented Federal Standard paint numbers that you can track down on the web. In fact most Western air force colours are fairly well documented, but Soviet and Japanese colours are a minefield. While there are some WW2 colour photos, particularly of US planes, the colour balance of these photos are often wrong. This site is a fairly good starting point for aircraft colours but don't treat it as gospel:
http://www.ipmsstockholm.org/colorcharts/colorcharts.aspA minor consideration is the scale distance effect. Imagine a landscape with green hills all the way to the horizon. The nearest hills look bright and the further ones get greyer and greyer, i.e. more desaturated. So the further away you are likely to be looking at the subject the more desaturated it should be to look right. Four engined bombers might need slightly more desaturation than small fighters since to frame a screenshot you'd need to zoom out more and your viewpoint is further away. In general though you'd only worry about this a lot if you are skinning something the size of a battleship.
Finally there is the issue of lighting effects in the game. AH3 introduced a whole load of different effects that made many of my AH2 skins look wrong to my eyes. For instance I found I needed to make the aluminium base colour I used a lot darker to prevent it looking washed out by all the lighting effects.
So in the end you may just have to adjust stuff until "that looks about right."