Mmhmm. Once you arrive back in Haven from the boar island, pull up your menu and check status, subject stats. Unless you had a REALLY pure run on CS1, you should see some numbers other than 0 there: those come from DataCrystal. If it's all zeros (again, unless you really did come from a 100% pure run of CS1), you did something wrong.
Also, remember, DataCrystal is not a "real" save. It's just carrying over a few story stats. Your level is always dictated to start at 11 in GT, because that's what I tended to be at by the end of my CS1 playthroughs. Level isn't carried over, nor is horniness, or slut mode. The idea is that it's a "fresh" start, with potentially some things lingering beneath.