Do the State and Local tax amounts adjust because of the renter's deduction for IN? This causes a difference from the W2 entries. Has anyone else had this experience?

Not sure what you are trying to do.  You need to enter your W-2 exactly as it appears in the federal return, including the amounts from all of the boxes on the W-2.  Information flows from the federal return to the state return.   If you are entering information for a renter credit, you will be doing that when you prepare the IN tax return. You do not change anything on your W-2 in regard to a rent credit.