I'm relatively new to Premiere and was hoping someone could help me with the issue.
I'm using a template and it utilizes wipe effect for transitions between images. I reckon the black patch problem is due to them. It also can be due to masks applied to the images (judging by the shape)
For a workaround I tried rendering with the software renderer instead of the CUDA renderer. Well, it did help with the patches, but now where there should be motion blur it shows as horizontal lines. I should note that this is not the interlaced vs progressive issue. Rendering is already progressive.
Also the black spots don't always appear on the same spot and frame. Each render can give different results.