Yes, they are behaving differently because of the lack of nutrients, including lactose, and possibly because of the presence of other chemicals in soy milk that aren't in dairy.
Kefir grains are a complex community of different types of lactic acid bacteria and yeasts which metabolize (eat) various nutrients/chemicals in their environment. Because soy milk is a chemically different environment than dairy milk, these communities function in different ways. Over repeated propagations in soy milk, you probably have cultivated a very different community in regards to species diversity and the chemical products.
As Liu and Lin describe here
, the kefir community members in dairy milk are eating mainly lactose, whereas in soymilk they are eating sucrose, raffinose and stachyose. As a result, the reproduction of the bacteria and the yeasts differs, as did the alcohol and lactic-acid contents of the end-product.
Because your question is a practical one, you might be interested to know that in that paper, the authors found that adding 1% sucrose (table sugar) or 1% glucose to the soymilk produced an end-product that more closely mimicked that of dairy milk. You could give that a try and see if it improves your kefir growth.