I'm not positive on this, but I'm guessing that the problem is ammonia, not the rocks.
I'm guessing that your tanks aren't cycled, as you say you pull your fish out and clean the tanks. This actually isn't necessary. When I had guppies as a kid, they'd always die within a year, and it was because I did pretty much the same thing as you: I'd clean the tank out periodically. Instead of doing a complete clean, you only need to replace some of the water and vacuum the gravel periodically.
http://www.fishlore.com/NitrogenCycle.htm (This article explains some of what I'm going to go into here)
With the number of fish that you have in a 10g tank, it's overstocked. With no nitrifying bacteria, it would take a matter of hours for the water to become toxic. Guppies are hardy fish, so it takes them longer to show the effects of ammonia poisoning, but it still happens as days change into weeks and weeks change into months. The addition of new rocks may have just been an extra stressor that pushed them over the edge.
The basic concepts of setting up an aquarium are:
1)Established
nitrogen cycle is a must. Cleaning the tank periodically creates a cycle of poisonous water/non-poisonous water/poisonous water/etc... which slowly kills the fish.
2)One inch of
adult fish per gallon of water. This means that you should consider all fish to be of the length that they will eventually grow. Otherwise, you end up with scenarios where the fish have grown and you don't have an extra tank ready for them. This is one of the reasons that people without big tanks are suggested to only get male guppies/platies/mollies, as a smaller tank can't support the constant stream of babies.
3)Weekly water changes of enough quantity to keep the nitrate levels under 20ppm.
There's more to it, of course, but these are the basic concepts and the most important. Because an aquarium, unlike a lake or river, is a closed system, we have to work to mimic the ways that nature removes toxins from the water.