I'm a bit late to this, so I'm glad you got your stones back fine.
I've been on a few geology and biology trips that crossed borders, and generally I think rocks were usually fine (the bigger issue was whether we could collect them from the sites or not). Sometimes their are issues with soil and water samples, so it would probably be a good idea to give the rocks a quick cleaning if they are dirty.
Same thing with plants, sometimes we could take bare-root specimens in okay, but that's a lot more of an issue.
It probably also helped that we were traveling with at least a couple PhDs doing fairly specific research, and sometimes they even had papers and permits and such.
I think in general, as long as you declare it, you probably won't get in trouble, but might get it confiscated. I'm not certain, and not a lawyer, so don't take my word on it.