This issue was fixed...
If you're having this issue make sure your islands are spawning below 110 as the skyblock nether is 127 blocks high. If your islands spawn above 127 they're above the top of the nether's bedrock layer, therefore the roof.
Any islands that are above 127 in the overworld will spawn above 127 in the nether.
You can copy a players island with worldedit, have them reset their island and paste it back.
[After you change config so they spawn lower, ofc]