V6 Layers Create Tile Errors

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We have a type 1 tileset, using layers (2-3 I believe). On V5, this doesn't happen, but in V6 it does.

It shows blackness on the layers almost specifically in this area, but also in other areas. These tiles are not just black. If you look at the screenshots, I uploaded them in order moving to the right. When you go on certain levels, it fixes them kind of on the previous or current level at random. Going back makes them come back for some, but not for all.

Is there a reason this is happening? I see people on here using layers, but haven't come across this error in searching. I'm not really sure how to explain it besides the above.

If someone has a solution please let us know, as we don't want to continue doing gmap levels and this happening everywhere then have to backtrack them all.