Um... Okay, I'm lost 
So... You removed the stencil from the canvas, but you're still getting a transparency effect from the tool, even on a new layer? Is that right?
I'd go through the following:
• Do you have any tracing images loaded? Is so, remove/hide it.
• Just to be sure you cleared all of your stencils from the canvas, go to
Tool > Stencil Options > Show All Stencils (
yes, it's important to show them first. I'll explain in a bit). Now go back and select
Tool > Stencil Options > Hide All Stencils.
○ I'm having you show them again, first, because it's possible you've run into a bug, where a stencil isn't appearing when it should. By showing them all, and hiding them again, it may fix it.
• Did you make any selections, with the selection tool? To be sure there aren't any present, select
Edit > Deselect all.
• You didn't mention which tool you were using to paint with. Some tools have
opacity/thinners settings on them. Be sure you've set them correctly, otherwise the colors may be transparent.
• Along the same lines, some tools have a special "
Blend Mode" setting. If the Blend mode isn't set to
Normal, a tool can appear to be transparent.
See if any of that helps. If not, perhaps you could provide the .ptg you're working, or at least a screen shot of the program with the stencil you're using, and the area you're trying to color in.