Alright, it looks like I forgot to apply the new stencil buffer code to the default UI shader... Try opening up STM UI.shader and replacing the Stencil section with this:
Stencil
{ Ref [_MaskMode] //Customize this value
Comp [_MaskComp] //Customize the compare function
Pass [_StencilOp]
ReadMask [_ReadMask]
WriteMask [_WriteMask]
}
Lemme know if that works! You might have to right click the shader and reimport it after doing this.