Take some media out of each bed with some water in a glass and let them sit for a day. Then test the PH of both and see if there is any difference.
Thanks. I tested, found the gravel acidic, added a bucket of limestone under the water spout for that bed.
To avoid issues like this you should find a PH neutral media so that you don't have to manage it over the life of the system. You would think that they might balance each other out but if the rock is basic or acidic it would seem to me that there would be "micro climates" where the balance is not achieved depending on the fluid dynamics of the grow bed.