Merge all Layers is Flattening Images.

So I've come across a problem where when I want to merge all visible layers. Instead of creating a new layer with all my adjustments below that layer, it flattens the image getting rid of all my adjustments below. This is a bit problematic because I want to create my own action and I need to merge all visible layers in this instant. It doesn't matter if I try the shortcut of <shift> <CMD> E or just go up to Layers and down to "Merge Visible" it flattens the layer. And yes, clicking on "Flatten Image" still flattens the image. I've tried uninstalling Photoshop and reinstalling, and it still does the same thing. I own TK Panels which does what I want to do, but when I hit record plug-ins like TK actions and Lumenzia register after you hit the record button.