I use a variety of paints and can say that a final flat coat at the end really ties it all together (or satin, or gloss...deepening on the look you want).
So, I would second the suggestion of using a final coating for your models.
There are TONS of threads on it, but if you want my opinon...
* best spray can - testors dullcoat
* best airbrush - model masters acryl flat
Do a few searches on "flat varnish" you will get hundreds of posts and ideas.
If you don't want to do this...make sure your touch up paint is the same as yourbase coat.
If its spray paint, spray a bit into a cup, and use that.