Schedule Variance Issue

Dear All, 

I am using Primavera P6 for making a schedule and put up a L3 schedule to the Client. Along with the schedule I also sent a Performance Measurement System which is on physical milestone bases. For instance

Engineering: 

Deliverable: at start = 10% , IFA = 60% and on IFC = 100%

I have used similar milestones for procurement and construction activities. 

I have cost loaded my schedule in terms of weightages to arrive at performance % complete. 

Now, when i report the progress variance, it is more than it should be. The Schedule % complete is always based on the cost assigned to task and duration tht i should have completed and shows intermediate %ages whereas i am claiming Performance % complete when an activity actually completes.

A small example is an activity which has already starting on 15 Dec 2010 having its finish date on 15 January. On data date of 31 December 2010, the schedule % complete shows 50% whereas Performance % complete is 0% at this time and will be 100% only on 15 January. So, I am not able to justify the variance. 

Please help on this issue and devise some work around for this matter.

Kind Regards,

Nouman