Estimate At Completion

I am having toubles calculating estimate at completion. I know the formula and the ways to calculate it, but the difficulty i am facing with it is that, the actual values i get from our cost reporting software is too low. the reason for it being too low is that, a subcontract activity gets paid 45 days after the claim is made, which increases the CPI for that month, this leads to a low overall Estimate to complete. Is there any other way to calculate it????? have any of you faced a similar situation.

thanks in advance
Karl