Yea, somewhere, one of your mods has removed the autoplace specification for medium-rocks, (which is just turning off their placement) ... the same mod likely modifies Nauvis to not spawn those rocks either... Nothing is telling this mod to expect that. There may be a way for me to check all of the placement rules and update them accordingly, but it will only work if my mod is loaded after their mod - mod ordering is often uncontrolled, or if I can do the check in the final updates step and their mod hasn't made the change during final updates.
If you can figure out exactly which mod is causing the issue, I'll do a fix if its possible.