OKay, what's happening is that when you are topping off with tap, you are adding TDS into your tank.
For instance- Let's say your tap is TDS 400. When water evaporates, the water is gone, but the TDS of 400 stays in the tank.
When you top off with your tap, the TDS in the new water is an additional 400, plus you are adding that to your tank of TDS 400 water. This is where teh TDS raises.
That's why when topping off, people use RO which adds nothing. TDS 0 (or nearly so.)
It's not the cuttlebone. At least it never happened when I was using them.