Link to mod? I can't find anything under "storage cubes", or anything with "cube" name in general. I have a strong feeling that this is the same problem as here where another mod modifies the recipe table in Data-Final-Fixes after my mod has already created reverse recipes. I can't know in advance which mods do this, but adding an optional dependency to the other mod from within this mod ensures that it loads after the other mod.
As far as I know, there is no simple way to exclude recipes from being accessed by this mod, except by making the name of the recipe and the name of the item different (a lot of work on the other mod's end) or by coding a system of exclusion (requiring effort on both sides, for little gain). Or just tell me the name of the other mod and I can update this mod to load after, easy peasy :D