HI ToonArmy from down under,
Not knowing what kind of paints you are using, it makes a difference, it's a little hard to say. Possibly, the solvent in the matt coat you are using is getting under your finish, it could do this and the usual result is an "Alligator hide" effect. Sometimes it gets less pronounced as it dries, sometimes not. How long did you allow between application of the matt and last application of color? Longer is usually better, as with most things in the hobby, anything good usually takes longer and requires untold and vast quanities of patience. I usually use something like an enamel base for the base color coats, Model Master's is the brand I use.
Once that dries, no amount of water based acrylic anything that you can apply is going to touch it, other than to add to the effects I desire to add on top of already hard and dry enamel. You can use the company that makes the acrylic paint's own form of matt or gloss depending on where you are at geographically. Remember to place all your decals on top of a gloss finish on the top of the color coats, before you try to do all your paint applied effects for shading and weathering. You want to age and dirty up the markings that were applied when it was still in a washed and pretty condition. After you seal your decals down with another coat of gloss, then you can get nuts with a darker color of the main color if it is a monochrome paint job, if you are going with a multihued camo pattern, a dark grey such as Polly Scale's Scale Matt Black is hard to beat. Since it's acrylic it doesn't affect the enamel base coats. Since you are using it as a wash, the gloss coat that seals the decals and markings, is an extra benefit in aiding the run of capillary action that happens when you touch the tip of a loaded with washed down paint, brush to the crevice you want to decorate. If you are going over an area with something like a grille or lattice type area, ie. engine vent covers, screened openings, wider is better in the brush choice. And as usual, when you get done making a mess and have sopped up the excess with the modeler's mop, a Q-Tip, you get to let it dry and get even drier, then wait just one more day, Then you can go ahead and go to the dry brushing part to highlight all the areas that you just covered up with all that nasty grime and gunk. This pops the details out and makes for that award winning look that you see here in our galleries. Once you get that done you get to apply that Matt coat that bugged you in the beginning.That seals down all the paint work and gives your dust layers and pastel chalk something to hang onto.
I usually scrape the chalks across the coarse section of an old sanding stick and collect a neat little pile of pastel chalk dust on a mini post-it note pad. I found a cheap, .95 US cents, make up application brush, and yes this does require you to either go into the cosmetics section of a store and browse around, or find a generous female member of your acquaintance to give one of her old ones up. They have long long thin fine bristles and are very soft, the feature that we're lkooking at is the amazing amount of chalk dust that they let you transfer, just like what the ladies do with that warpaint and face powder that they all love to spend our monies on, monies I feel would be much better spent buying the old man a new model! Anyway, one thing to make sure of when you buy your pastel chalk is that you get the type that is chalk, just like the old school teacher's favorite that they spent so much time scratching on the chalk board in school. There is another type that has a greasy sort of base and when you try to turn it into chalk dust, you get a little pile of crumbles on the pad and a bright color streak that fills the sanding stick right up, to add insult to injury, when you try to apply it in the usual manner, it makes a solid color transfer instead of the see through effect that we are trying to duplicate.
Well I hope this helps you out, check out the threads that run through the painting issues forums here and check out the Rivet Review Board posts to see how some of these effects are used and for more info on how they are applied. Good luck on the Challenger, post us some pictures.