Very Slow Payment Proposal for Centralized Payment

Hi,

We are running AX on 2012 CU3. I have set up the centralized payment with two legal entities and have followed all the Microsoft instructions. After processing an invoice in legal entity of invoice I run the payment proposal in the legal entity of payment. However the process takes a long time. The dialogue box shows an estimated 60 minutes to run the proposal for only one invoice from one legal entity of invoice. After running the procedure for about 60 minutes still the estimated remaining time is 25 minutes. 

Is this a known issue or is it something I am missing. 

Thanks,

Reza