What paints were you using? I have been through all those painful problems as well. In my case I settled on painting using spray cans, using something NOT advertised as quick drying and preferably oil-based (hard to find), and pulling the stencils as soon as possible. I did some testing withe letting things dry thoroughly like you did but my results were not great, the dry film lapping up onto the stencil pulled paint off as well but in smaller little chips.