So answered my own question. Layers cannot currently have effects
For Reference here is the offending code.
// If rendered to texture, paste to main display now
// Drawing at layer opacity
ctx.globalAlpha = this.opacity;
ctx.drawImage(layer_canvas, 0, 0);
// Restore 100% alpha
ctx.globalAlpha = 1.0;
I'm about to install r69 and if I'm still not able to add layer effects I'll add in the code myself and post it here for all.