I have a short watercurrent which leads into a hopper an a dropper-item-elevator... after the elevator the items travel into a chest an then further through some more hoppers and get stored in chests...

If you put some cobblestone walls in the watercurrent, they'll turn into Cobblestone blocks somewhere before they enter the last chest.

I've tried to find where they turn to cobblestone but then suddenly it worked perfect...
Seems like the bug only shows off sometimes...