What brands of paint are you using? Drying time on some paints is much faster. Even if you're using the same mfg., are you using the same type of paint all of the time? Try using the same brand of thinner with the paint and see if that helps.
How much are you thinning your paint, and is it completely mixed in the bottle before you thin it? In some brands, the pigments tend to congeal (sp?) and may need more mixing. As another psoter asked, is your brush gravity or siphon feed. The brush type will affect the pressure that you need to get the paint out. How long are you painting at one time? I find that all paints tend to dry faster than I would like. If possible, don't leave paint sitting in the brush too long. It can start to dry on the surface and small glogs can form.
I have two Iwata's and have no problems with them, except one time when paint worked its way into one brush's trigger mechanism and made it sticky. Don't know how it happened and it only happened once. Finally, while it may not be an option for some people, if you have to paint two colors very quickly, it is better, IMO, to have two brushes with a different color in each one. It allows you to apply paint now and clean up later. I've posted this photo in another thread, but I'll do it again. I use a Harder & Steenbeck manifold that connects to my compressor. Each of my AB's has a quick connect so they can be changed easily. This way, when needed, I can have two or three colors ready to go.