If you bring in an image or video into Shotcut that does not have the same aspect ratio as the project’s video mode then when Size & Position is applied the image or video is thrown away from the center.
So for example this image here:
This may have become an even bigger issue now with the Slideshow Generator because there is a bug I am coming across where video clips are not producing the animations that they are set to and stay still. These video clips have aspect ratios that are different than the video settings. When I select the individual clips I see that the S&P rectangle VUI is off from where the video actually is just like I shown above the the Yin Yang image. Here are examples: