Stitching Issues

[Tas-V]

I am trying to stitch a brain that had wobbly scanning but am not getting good results. I am facing two problems:

1. Black tiles
2. misaligned outer cortex at tile overlap in some tiles

I have included pictures of both issues; the second issue in particular is strange, as it seems that the wobbly stitcher is not moving tiles in x/y from the rigid alignment. It has determined that the misaligned area seems to be the best area. I have tried skipping the rigid stitching step but still face the same issue. Are the cells too dense for proper stitching to be done?

img1: rigid stitching preview
img2: wobbly stitch image (no rigid alignment), misaligned outer cortex and black tile