Did you try resetting the Photoshop prefernces? First try that.
If that doesn’t work then try removing the clipping shape and using the layer mask instead. Just put the rectangle into the layer mask. That is how it is suppose to be done for SPA anyway. The way you are using the clipping on works for player modes 9/10 and ONLY if you are also selecting the smart objects checkbox in the settings. However, it isn’t the right way to add transparency for SPA regardless.
If removing the shape layer doesn’t work then try recreating the PSD from scratch.