How did you save the image for the stencil? I have the best luck saving stencils, overlays, and the base texture as PNG images and letting TSRW do the converting itself.
Which stencil slot did you upload it into? A through F or whatever it is...
Also the stencil won't apply to every color option for the shirt unless you manually do that.
If you're still having issues I can try looking at the file myself if you want to hand it over. I'm not a TSRW expert but I have enough familiarity with it.