From Ian Schnack, here's the method for adding new rows in the Windows tab in PHPP so you don't get a bunch of linked rows (don't ask me how I learned this):

Thankfully the solution is pretty simple (that is if I am understanding you correctly). Here what you should do next:
-For each of the new drop-down boxes you created, you will need to change the reference cell the drop-down is linked to
-right-click on the drop-down and select 'format control'
-make sure the 'input range' correctly covers the newly inserted cells and change the 'cell link' to correspond correctly
-then hit ok - you'll need to do this for all of the new drop-downs, the rest should have updated themselves when you inserted the rows (but I would check just to make sure)
-also, unhide all the cells to the right and copy the formulas down to the ensure the new inserts are calculated properly.
-lastly, make sure to update the shading and shading-s pages as well