I finally got a solution to the NY Partnership depreciation adjustment not being populated to the IT-225 and IT-398.  The fixed assets causing the issue are QIP, and there is a box to check, to indicate that.  Also, you have to put in the 39 year state depreciable life, which indicates to the software that it is QIP.  Even in doing all that, the depreciation expense itself is correct for both Fed and NYS, but the differences weren't being populated...until I uncheck the QIP box.  Then it populates correctly.