I've been looking for the shrines and finally found one, broke the stone and that's it. What a huge disappointment. Found two more, broke the stone, nothing else.
It should be noted that the shrines were completely new and that I'm playing on a server. It should also be noted that it used to work.
I am using the latest version for 1.12.2

I don't have those kinds of mods. There is no claiming mods or anything.
List of mod:
10/02/2018 14:02 55,893,034 AmbientSounds+v2.2.2+mc1.12.2.jar
10/02/2018 13:51 32,317 AppleSkin-mc1.12-1.0.9.jar
10/02/2018 13:45 16,332,798 astralsorcery-1.12.2-1.8.5.jar
10/02/2018 13:55 506,667 base-1.12.2-3.6.1.jar
10/02/2018 13:56 1,962,731 bdlib-1.14.3.12-mc1.12.2.jar
10/02/2018 13:53 75,709 BetterBuildersWands-1.12-0.11.1.245+69d0d70.jar
10/02/2018 13:47 155,196 BetterFps-1.4.8.jar
10/02/2018 14:04 5,148,425 BiblioCraft[v2.4.3][MC1.12.0].jar
10/02/2018 13:49 4,868,866 BiomesOPlenty-1.12.2-7.0.1.2313-universal.jar
10/02/2018 13:50 244,613 Bookshelf-1.12.2-2.3.523.jar
10/02/2018 13:45 472,782 BrandonsCore-1.12-2.3.7.140-universal.jar
10/02/2018 13:57 4,284,190 buildcraft-7.99.14.jar
10/02/2018 13:43 96,859 Chameleon-1.12-4.1.3.jar
10/02/2018 13:47 314,060 ChestTransporter-1.12.2-2.8.8.jar
10/02/2018 13:54 132,232 ChickenChunks-1.12.2-2.4.1.71-universal.jar
10/02/2018 14:46 17,346,525 Chisel-MC1.12-0.1.1.24.jar
10/02/2018 13:51 695,675 chiselsandbits-14.13.jar
10/02/2018 13:55 13,778 Clumps-3.0.0.jar
10/02/2018 13:45 650,693 CodeChickenLib-1.12.2-3.1.5.331-universal.jar
10/02/2018 13:57 764,904 CoFHCore-1.12.2-4.3.10.5-universal.jar
11/02/2018 20:05 399,333 CoFHWorld-1.12.2-1.1.1.12-universal.jar
10/02/2018 13:42 181,856 CTM-MC1.12-0.2.3.12.jar
10/02/2018 14:08 722,552 CustomMobSpawner-3.11.3.jar
10/02/2018 14:35 65,319 cxlibrary-1.12.1-1.6.1.jar
10/02/2018 13:49 448,983 DarkUtils-1.12.2-1.8.193.jar
10/02/2018 13:54 863,205 deepresonance-1.12-1.6.0.jar
10/02/2018 13:45 5,552,107 Draconic-Evolution-1.12-2.3.8.279-universal.jar
10/02/2018 14:18 22,443,630 DrZharks MoCreatures Mod-12.0.3 (1).jar
10/02/2018 13:54 845,761 ElecCore-1.12.2-1.8.434.jar
10/02/2018 13:51 221,404 EnderStorage-1.12.2-2.4.2.126-universal.jar
10/02/2018 13:59 244,973 endertanks-1.12.0-1.6.3.jar
10/02/2018 13:53 3,779,552 ExtraBitManipulation-1.12-3.2.1.jar
10/02/2018 14:02 9,099,190 ExtraPlanets-1.12.2-0.2.1.jar
10/02/2018 13:42 2,885,143 extrautils2-1.12-1.7.3.jar
21/02/2018 20:19 0 filename.txt
10/02/2018 13:55 421,631 fluxnetworks-1.12.2-3.0.3.jar
10/02/2018 13:41 3,820,398 Galacticraft-Planets-1.12.2-4.0.1.132.jar
10/02/2018 13:39 10,302,770 GalacticraftCore-1.12.2-4.0.1.132.jar
10/02/2018 13:56 1,674,251 generators-0.9.20.12-mc1.12.2.jar
10/02/2018 13:50 76,022 gravestone-1.10.1.jar
10/02/2018 14:37 164,579 Guide-API-1.12-2.1.4-57.jar
10/02/2018 13:46 446,657 Hwyla-1.8.23-B38_1.12.jar
10/02/2018 13:57 550,812 iChunUtil-1.12.2-7.1.4.jar
10/02/2018 14:32 7,235 ImmersiveEngineering-0.12-76-core.jar
10/02/2018 13:42 5,937,804 ImmersiveEngineering-0.12-76.jar
10/02/2018 13:42 262,219 InventoryTweaks-1.64-dev.jar
10/02/2018 13:42 1,097,937 ironchest-1.12.2-7.0.34.820.jar
10/02/2018 13:50 545,366 jei_1.12.2-4.8.5.151.jar
10/02/2018 15:26 1,822,850 journeymap-1.12.2-5.5.2.jar
10/02/2018 13:50 215,140 JustEnoughResources-1.12.2-0.8.7.41.jar
10/02/2018 14:01 181,970 Level+Up!+2-1.1.15-1.12.jar
10/02/2018 14:00 773,275 lostcities-1.12-2.0.1.jar
10/02/2018 13:43 865,513 Mantle-1.12-1.3.1.21.jar
10/02/2018 13:47 366,615 mcjtylib-1.12-2.6.3.jar
10/02/2018 13:52 163,254 MCMultiPart-2.4.1.jar
11/02/2018 19:44 15,993,190 Mekanism-1.12.2-9.4.3.330.jar
11/02/2018 19:49 338,420 MekanismGenerators-1.12.2-9.4.3.330.jar
11/02/2018 19:49 161,111 MekanismTools-1.12.2-9.4.3.330.jar
10/02/2018 13:39 50,849 MicdoodleCore-1.12.2-4.0.1.132.jar
10/02/2018 13:59 27,940,497 minecolonies-universal-1.12.2-0.8.7494.jar
10/02/2018 14:35 80,014 MJRLegendsLib-1.12.2-1.0.6.jar
10/02/2018 13:48 870,528 MobGrindingUtils-0.3.4.jar
10/02/2018 15:13 162 mod_list.json
10/02/2018 14:01 121,463 MoreFurnaces-1.12.2-1.10.5.jar
10/02/2018 14:01 10,710 moreloottables-1.12.0-0.1.0.jar
10/02/2018 13:57 1,018,651 Morph-1.12.2-7.1.2.jar
10/02/2018 13:42 20,837 Morpheus-1.12-3.3.2.jar
10/02/2018 13:53 3,148,569 OpenBlocks-1.12.2-1.7.5.jar
10/02/2018 13:53 2,609,119 OpenModsLib-1.12.2-0.11.5.jar
10/02/2018 13:46 2,219,800 RandomThings-MC1.12.2-4.1.2.jar
10/02/2018 13:45 33,436 RedstoneFlux-1.12-2.0.1.2-universal.jar
10/02/2018 13:49 1,750,553 refinedstorage-1.5.31.jar
10/02/2018 14:00 53,918 refinedstorageaddons-0.2.jar
10/02/2018 13:56 1,206,299 Reliquary-1.12.2-1.3.4.733.jar
10/02/2018 13:51 2,878,703 rftools-1.12-7.27.jar
10/02/2018 13:49 573,359 rftoolsctrl-1.12-1.8.0.jar
10/02/2018 13:46 1,671,994 rftoolsdim-1.12-5.51.jar
10/02/2018 13:59 395,298 shetiphiancore-1.12.0-3.5.6.jar
10/02/2018 14:00 87,465 simplegenerators-1.12.2-2.0.7a.jar
10/02/2018 13:55 1,161,406 sonarcore-1.12.2-5.0.5.jar
10/02/2018 14:00 264,741 SoulShards-TOW-1.12-2.7.4-53.jar
10/02/2018 13:43 590,377 StorageDrawers-1.12.2-5.3.4.jar
10/02/2018 13:54 402,870 StorageDrawersExtras-1.12-3.1.0.jar
10/02/2018 14:01 1,520,219 taiga-1.12.2-1.3.0.jar
10/02/2018 13:43 3,747,716 TConstruct-1.12.2-2.9.0.55.jar
10/02/2018 13:55 30,925 Tesla-1.12.2-1.0.63.jar
11/02/2018 19:43 716,384 ThermalDynamics-1.12.2-2.3.10.4-universal.jar
11/02/2018 20:02 2,022,699 ThermalFoundation-1.12.2-2.3.10.6-universal.jar
10/02/2018 13:57 159,350 TinkersComplement-1.12.1-0.2.2b.jar
10/02/2018 13:48 91,796 TinkerToolLeveling-1.12-1.0.3.jar
10/02/2018 14:01 644,751 tinyprogressions-1.12-3.2.10+-+Beta.jar
10/02/2018 14:01 6,899,106 twilightforest-1.12.2-3.6.345-universal.jar
10/02/2018 14:00 275,550 valkyrielib-1.12.2-2.0.7a.jar
10/02/2018 13:59 128,682 VeinMiner-1.12-0.38.2.647+b31535a.jar
10/02/2018 13:45 31,462 WailaHarvestability-mc1.12-1.1.12.jar
10/02/2018 13:48 81,117 Wawla-1.12.2-2.5.251.jar
10/02/2018 13:59 526,210 woot-1.12.2-0.0.8.jar
11/02/2018 19:43 418,122 xnet-1.12-1.6.7.jar

In order:

• Check /config/astralsorcery/treasure_shrine.cfg and make sure at least a few different ores are listed there.
• Try in a new world.
• Try with just AS alone
• Try adding more and more mods and try reproduce with a new world in each until you can reproduce the behavior.

I here can't reproduce the issue nor has anyone else ever reported this.

The thing is, there are ores listed, the shrines worked earlier, and now they don't. My server is up 24/7

What'd you break it with, and were you nearby when doing so, or did you use a machine to do it?

The first shrine, I used a builder from RFTools, the next i used regular pickaxes, iron and a third shrine i used a vanilla diamond pickaxes. I flew over to the shrines in spectator mode. But they were newly loaded.

What mods are in-use/modpack? Sponge? Did you claim the chunk? That's not normal behaviour.

Maybe try restarting the server, then.

@BleesTFE any update?

A player on my server has encountered the same bug on the Enigmatica 2: Expert modpack, ver. 1.26c, and I confirmed ores show up, but blocks don't drop in multiple treasure shrines. Tested with Tinker's, vanilla, BM, Mekanism's Atomic Disassembler, as well as a Cardboard Box (item disappeared, no box showed up, block changed from an ore to stone).

The shrines weren't claimed, no Sponge or anything similar.

Can you narrow it down? Again, never reproduced and I know of several servers running that pack and version that didn't have this issue.

Does the Treasure Ore/Stone have a codename?

I'm working on narrowing it down, I'll let you know if I come up with anything.

So it seems Tool Progression is the cause of this bug, at least for me (I know I'm in creative, but you can see the difference):
Without: https://imgur.com/a/vDKf4fc
With: https://imgur.com/a/MVeWDN2

I suspect the Treasure Ore/Stone is a special block that contains other blocks, so I need add a harvest level to the "container" - Is that the case, and if yes, by which name do I reference it?

This is the TE that handles it all: https://github.com/HellFirePvP/AstralSorcery/blob/master/src/main/java/hellfirepvp/astralsorcery/common/tile/TileOreGenerator.java

I'm not sure how you're handling it on your end, but I don't think that will be useful.

Yeah you're probably right, I'll take it up with the Tool Progression dev.