I dont think the installment agreement application request is really integrated into the tax return itself. 

Ive stopped including it with returns (it just takes too many months for it to be processed when you do it that way) and have the client wait for the return to post to their account then apply for the installment online or over the phone.

I have noticed that it takes a while for the Installment to kick in, thanks for the tip.

I did figure out that the differnce in 1040X in this case was that the refund recieved originally had to be added to the installment, Line 6.

Thank you very much for your reply.