Possible Reasons why the Std Cost Roll differs from the Cost BOM Rpts
The values displayed should be in sync with the BOM with Std Cost Report  values.  The following may be why the Standard Cost Roll is different from the Cost BOM Reports.

a)    On the costed BOM Report for a Make/Buy assembly we display the value of the BOM in the costed report, but that total is NOT used in subsequent rollups to higher levels only the standard cost is.  

b)    In Kit Default Setup , user can exclude scrap and setup scrap in Kitting, MRP, and Cost Rollup, this will overwrite what user check in the BOMTherefore, if user checks "Setup Scrap" checkbox in BOM, but checks to exclude in cost roll, the costroll will not calculate setup scrap cost, but BOM will always calculate setup scrap cost if the Setup Scrap checkbox in check in BOM.