Hermann's, right? I think you're keeping his substrate too wet. You need to find a substrate that dries out on the top layer, yet stays moist underneath. Those spots MIGHT be the start of shell rot from being kept on moist substrate.
You must remember that Tom's threads talk about sulcata and leopard tortoises, and don't really pertain to the testudo species of tortoises. You can PM GBTortoises and give him a link to this thread. He's very good with the Mediterranean tortoises.