The fortune 3 pickaxe does return flint for every gravel as well. No issues with fortune 3 either
Tried my pickaxe on iron ore and lapis and the same issue applies. The same pickaxe seems to work just fine for harvesting potatoes and drops like 5 potatoes per plant. My fortune III shovel returns flint from every gravel, so thats not an issue either.
I did more testing:
Same fortune 3 pickaxe seems to work on melones normally. Harvested 7 melones with the following drops: 9, 5, 9, 8, 5, 8, 5
Changed the difficulty from hard to peaceful and tried the same pickaxe fortune 3 with copper ore blocks with the following drops: 15, 9, 20, 2, 8 → seems to work nomally.
Changed back to hard with the same pickaxe and copper ore with the following drops: 2, 11, 3, 4, 12. Not impossible with fortune 3 but significantly less than usual