While investigating the absence of rocks in places where there should be rocks, I discovered that the type of terrain where one would expect to find rocks was mistakenly (I assume) set up in the foraging lists to look for photophobic fungus instead. You may now find rocks in places where they have not been found before. While I don't know of any areas which are specifically set up to actually be photophobic fungi-infested areas, it is possible that you may stop finding rocks there.

-Tarragon