BigStitcher black square

Has anyone had a problem like this? It seem to appear during image fusion step. BigStitcher creates a black square in the middle of the image. I also stitched these tiles myself and the result didn’t show such an artifact.

This is the result from BigStitcher

This what I expect in terms of illumination

Could this be due to some sort of normalization?
The input data is uint16 and I also save it as uint16.

This is the fusion settings that I use

    // fuse dataset, save as TIFF
    run("Fuse dataset ...",
        "select=/output/best_focus/Cyc002_Reg001_CH001/dataset.xml" +
        " process_angle=[All angles]" +
        " process_channel=[All channels]" +
        " process_illumination=[All illuminations]" +
        " process_tile=[All tiles]" +
        " process_timepoint=[All Timepoints]" +
        " bounding_box=[All Views]" +
        " downsampling=1" +
        " pixel_type=[16-bit unsigned integer]" +
        " interpolation=[Linear Interpolation]" +
        " image=[Precompute Image]" +
        " interest_points_for_non_rigid=[-= Disable Non-Rigid =-]" +
        " blend produce=[Each timepoint & channel]" +
        " fused_image=[Save as (compressed) TIFF stacks]" +
        " output_file_directory=/output/processed_images/Cyc002_Reg001_CH001");

This problem appears during pairwise shift estimation. The global optimization step moves discarded tiles to the 0,0 position on stitched image, and because these discarded tiles are dark the resulted average of them with tile at that position is also dark.