That certainly is odd...you may want to ask a question here:
I'm sure someone there knows more about that specific problem.
For me, Hisui and Kohaku were paired together until I was either able to beat or play the Hisui route (I forget which). Then they separated into their own CG modes.
On day 1, you don't have "元気だった女の子のことだ。" as a choice during the 4th decision?