Check this blog it helped https://scn.sap.com/thread/1453048
I finally found the time to review this problem again and have now resolved the issue of the zero actual cost rolling up from the Work Orders. The key problem was that the reports read the secondary cost elements from the settlement which are the credit side of the settlement hence the zero.
The resolve this you have to suppress the secondary cost elements with another value category using transaction OPI1.
Then you assign the cost elements you want the reports to suppress in transaction OPI2. Then select "Supress"
Run CJEN for the project and the actual cost will roll up.
Thanks for everyone's help.