The dust of ender pearl that is added by Railcraft is registered in OD as dustEnder. Most mods use dustEnderPearl instead. That causes some incompability with Railcraft. Maybe additional registration can be added or completly changed?

For now use crafttweaker to bypass this restriction.

I registered everything correctly. Then I tried to fix the recipes.

#Fixing ender pearl dustFertilizer
recipes.replaceAllOccurences(ore:dustEnder, ore:dustEnderPearl);
recipes.replaceAllOccurences(railcraft:dust:6, ore:dustEnderPearl);

That's lead to a recipe in which void powder is made of three ender dust instead the normal recipe. Don't know how this could happend.

I guess crafttweaker has some issues with item meta. Cannot help beyond that,

That only effects Railcraft. No other mod though.

Please list some mods. Afaik, some mods use dustEnder, including not enough potions mod,

-Ender IO
-Applied Energestics 2 (uses both in recipes as alternatives)
-Tech Reborn

I guess crafttweaker has some issues with item meta. Cannot help beyond that,

That couldn't be a problem with metadata. The recipes uses dustObsidian for instance. It seems that Crafttweaker finds the right recipes and assumes that every ingredient is railcraft:dust:6 instead of just one.

It might be adding ItemDust to the oreTag as a wildcarded ItemStack, matching everything.