Standard Cost Updates Result in Bad B2 Cost

We are on JDE 9.3 using discrete manufacturing with standard cost.  We upgraded to this version last February (2014).  We try to run standard costing once or twice a year when most everyone is off the system and try to make sure most work orders are closed. We have noticed since the upgrade that some of the orders that are not closed during a cost update, end up with large engineering variances specifically within the B2 cost.  The standard (or frozen cost) is always grossly inflated after the update.  Have others experienced this?  We have several hundred work orders a