This is why you ALWAYS shoot on a test panel before you shoot your final. I would say either the paint is either A - not mixed well enough, or B - getting humidity introduced. I have shot all kinds of projects with the Lowes Graco sprayer; from restorations of tractors, priming cars, redoing bathrooms, etc. with outstanding results. Specifically the Graco 2900. I shoot enamels, lacquers, oil based, you name it. All have come out great if you take your time, and remember that several light coats will look better than heavy coats. Do not rush painting, ever.
That being said, I would make sure all the parts of the gun are clean, and test with water on something, like the garage door. Get the technique down, then clean the gun and let it dry, and follow the same technique with the paint. Provided your paint is a similar consistency as the manufacturers recommendations, you should be fine. Start off the edge of the panel and continue spraying off the panel, to maintain consistent coverage. Dont rock your wrist, keep the gun parallel with the work. And for goodness' sake if it looks bad, STOP. Don't keep going. Assess the issue, correct it, test it, and keep painting.
Don't let a couple runs put you off. I have a 2x4 with about a zillion coats of primer and paints I use for testing just to avoid issues. Keep it up, you'll get it and you'll totally be proud of your final project \m/