I've found dimlet for Dimensional shard ore, and tried to combine it with terrain dimlet. Used flat terrain dimlet, islands, solid, and every single time i get worlds, made of forestry's wenge stairs. Tab with only dim. shards ore seems not use this dimlet at all.
Here is what this dimlet is, as crafttweaker says:
rftoolsdim:known_dimlet:2.withTag({dkey: "rftools:dimensional_shard_ore@1"})
I'm running LAN singleplayer on Modern Skyblock 2 modpack.
mcjtylib-1.12-2.6.2
rftools-1.12-7.23
rftoolsdim-1.12-5.50
forestry_1.12.2-5.7.0.234
forge 14.23.1.2587

I've just checked without forestry, and it just replaces orbs or tendrils with air or some other block, like dirt, prismarine, etc. With only RFTools and COFH mods, it works as intended. Seems some weird id conflict is happening. But it's over 100 mods, so I even don't know where to look first to find conflict =(

Try doing a binary search. It'll only take 7 or 8 tries to find which one it is.

I'll try to make completely clear copy of modpack in the morning, without crafttweaker scripts, and maybe, catch problem mod. I have a slight suspicion that it could be the progression, that messes it all up.

Ok, I've done search, and found 16 mods either replacing dimension shard ore with other vanilla or modded block, or replacing it with air. And now the point, where I don't know how to fix it not deleting mods, cause modpack does have quest progression. Here is the list:
EnergeticSheep-1.12.2-1.1.1
environmentalmaterials-1.12.2-1.0.6a
environmentaltech-1.12.2-2.0.6b
etlunar-1.12.2-2.0.6a
EvilCraft-1.12.2-0.10.44
extendedcrafting-1.12-1.1.3
ExtremeReactors-1.12.2-0.4.5.45
generators-0.9.20.12-mc1.12.2
Immersive HempCraft-1.12-0.0.4.0
industrialforegoing-1.12.2-1.7.0-114
industrialmeat-1.12-1.0.2
IntegratedDynamics-1.12.2-0.10.1
IntegratedTunnels-1.12.2-1.4.1
IntegrationForegoing-1.12-1.4
ironchest-1.12.2-7.0.34.820
valkyrielib-1.12.2-2.0.6b

Just forget the progression for now, for the sake of figuring out which mod is at fault. Once you get it down to one mod that causes it, we should be able to easily fix it.

I did it!
It was RebornTeam mods, probably their coremod, RebornCore. There are 3 mods, dependant on this coremod in pack I'm playing, so I can't check if it is coremod or actual mods. Here are names and versions of mods, causing problem:
RebornCore-1.12.2-3.6.2.187-universal
SolarFluxReborn_1.12.2-3.42r
StevesCarts-1.12.2-2.4.16.81
TechReborn-1.12.2-2.11.1.420-universal

Awesome that you got it that far! We should be able to figure it out from there.

Thanks! Will be waiting for fix =)

Here is list of mods when problem is present: https://gist.github.com/aerde/08b944b30c9af29f20c917a230475c9d

It's been a while, since I've began testing, so some mods got updated. And probably, I messed up, and in the list are couple of mods I didn't include in testing... I'll check this tomorrow.

I've blamed NotEnoughIDs too, but without it, modpack doesn't work. And it doesn't seems to have a config file.

That's a lot of mods still. How did you narrow it down to a *Reborn mod with all of those still present?

I think it is a NEID problem. It should be fixed in the next release of RFTools Dimensions.

EDIT: I just tried in Modern Skyblock 2 and confirmed the fix, so it will work next release.

Note that Solar Flux Reborn is actually a HammerCore mod, not a RebornCore mod. What version of HammerCore did you experience this on?

Also, I can reproduce this with all of Modern Skyblock 2, but not when I disable all mods except the ones you listed. Can you post a mod list of everything that you left enabled?

And I wonder if this is related to NotEnoughIDs. Maybe the problem only occurs if you get enough that its changes matter.

Cool! Thanks a lot) This problem was draining my powers))