I have had more than one stand-alone Nupoint on 3300's with digital phones, and it has never been a problem since there is no SDS sharing, or any kind of sharing of data, that occurs between the two boxes.
How are you building the mailbox?!?! Are you just adding mailbox 1234 in Nupoint's web console for digital extension 1234 and this error is coming up? Dumb question, but in the SS4025's COS you do have the HCI options enabled, correct?