I have a Gemini Junior and I admit to little success in stopping the warping of the clear acrylic plates. I read a post somewhere, recommending the use of this protocol for the Gemini Junior:
1. Clear, never-used cutting plate on the bottom
2. Then place the die, cutting side up, (taped to secure if necessary)
4. Then shims (magnetic and plastic)
4. Then grungy (warped) clear cutting plate on top, always mountain side up.
I had a lot of success with this, but I've had vastly improved outcomes by replacing the magnetic and plastic shims with the new Magic Mat.
Dies cut cleanly and usually in one pass.
If the Magic Mat starts to warp, a quick blast of the heat gun on the warped spots and the mat seems to return it to its flat state.