Always thin (or reduce) a paint for spraying unless it is one of the "pre-thinned" varieties.
Your problem could be caused by undispersed flat pigment (flat finishes are produced by a pigment), surface contamination (a small dust particle can create a local electrostatic charge concentration that will attract the flat pigment or the binder), or contamination of the thinned paint. This latter would be due to an incompletely cleaned air brush or use of tap water as your reducing solvent.
I suspect the cause is the first possibility. Flat pigments tend to clump during storage. Clear flats should be stirred very thoroughly (five minutes by hand, minimum; less with a powered stirring device). Never shake small bottles of any paint to mix it. They are not large enough for that to work efficiently—always stir.
Reducing (thinning) a paint also helps to insure adequate dispersion of pigment. A rule of thumb is to thin to the consistency of 2% milk. For clear coats, erring on the side of more thinner is better than too little.