Keith,
I take it from your post that you're hand brushing the topcoat on - and not using an airbrush?
If that's the case, Tweety has a couple of good ideas -
1. Make sure the paint is properly stirred to completely mix the pigments with the
carrier.
2. Always use the correct brand of thinner for the correct brand of paint. I've also found that Model Master thinner to work well with many different types of enamel paints.
3. Decant a little paint into a jar lid (or something similar) and thin the paint a little to help the paint "flow". Thin the decanted paint, and NOT the paint in the bottle, as the change in chemical ratios (once thinner is added) can drastically shorten the shelf life of the paint. I've had bottles turn to gel in a couple of days.
Properly stirring and then thinning the paint with the right thinner will help a lot.
Also, why not think about trying an airbrush? There are quite a number of relatively inexpensive units in the market. Many smaller air compressors can be pretty cheap as well. If you want to try it but need more advice, try one of the Kalmbach Scale Modeling Guides - (see the link on the left of this page) - the books are very good and there are a couple on basic airbrushing.
Good luck!