It's probably emulsion residue which is drying in your stencil. After washing out your screen, water droplets on the squeegee side of your screen picks up uncured emusion and settles in your stencil. As it dries, it leaves a thin film, preventing ink from passing through.
After washing out your screen, run your finger on the squeegee side of the screen. If it's slimy, that means it's not fully cured. You need to increase your exposure time. I had the same problem, however when I tried inceasing the exposure time, I had a difficult time washing out my design. I had to resort to using an air compressor to blow out any water in and around my stencil. I have since made my own exposure unit with a 1000 watt metal halide bulb. That has taken care of the problem. Now I get clean clean washouts, with no slimy residue on the backside, no residue in my stencil.
Hope this helps.