I’m having this same issue (watermark applied to all images except the full image).
Details:
* I’m compressing/optimizing images automatically using ShortPixel (they recommended your plugin)
* After compression I manually apply the watermark (png) to my images (png)
* Watermark only shows up on thumbnail and the other sizes, not the full size image
* No watermark appears on auto-watermark either
Watermarking was working before I tried combining with ShortPixel.
