Had the same problem in my mod pack with the recycler-recipes: one item + fluid, the problem here was that my assembler prototype for this recipes had an "ingredient_count=1", the game engine dosen't care about it, aslong one of the two ingredients is an fluid so it was useable. But FNEI dosen't show it, after chaning "ingredient_count=2" as it suposed to be, FNEI shows the recipe.
Maybe it's the same problem?