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For some reason, there isn't a beyond.zs file in my scripts folder, yet it still makes the recipes.
Gif: https://gyazo.com/10b751e539e5296fd4a004ed5e9b3262
Looks like it's biome related, as you said, you added an external mod, BiomeBundle. IC2's Rubber wood & saplings are trying to be placed in some kind of biome, but crashes instead. Report it to the author of BiomeBundle.
Crash logs /logs or closed.
-An extra mod isn't considered FTB Beyond, so no support, but logs will still be appreciated, hence it might still be able to help.
I don't see a bug here. Nearly any food related items can be inputted to it, meaning even Natura bush's fruits (which can easily be automated) + Yogurt (Which can be produced infinitely with a cow being milked by a Mech. user set to Entity, pumping buckets into a Mech. crafter to make milk...
The black flowers from Actual Additions can be turned into ink sacs or black dye, whichever works as the same.
Edit: Unless the item has to be ink sacs, then, well, rip.
http://www.minecraftforum.net/forums/minecraft-discussion/survival-mode/227323-stuck-in-bed-bug - 2011
https://github.com/whatthedrunk/allthemods/issues/43 - Says Vanilla
https://www.reddit.com/r/Minecraft/comments/23cq65/another_mincraft_bug_cant_get_out_of_bed_after/ - 2 years ago
Oh so many...
Before deleting the world, try delete random things first, and then enderIO. If nothing, then it's truly corrupted. I'm also truly sad for whoever has only put 2 Gigs of ram to their client or/and the server. Server needs a BARE minimum of 4 for a vanilla server.