I think this may be the problem we are having.  
We found that if you typed in the GL account ont the purchase order then if the invoice amount was different it went to the WIP default account, but if you accepted the part number's item class and left the Purchase Order line GL account blank them then it would go to the default account.    Even if you type in the same GL account associated with the part number it defaults to the WIP asset account.  If you type in a GL account on the PO line it will no longer distribute the different to the item class.   You have to leave the GL Account on the PO blank if there is a chance the vendor's invocie will not match the recieving.  The only way I can get the line to properly distributed is to leave it blank.   I was hoping to be able to use the Override on each PO line, but can not since it ends up sending discrepancies to the default account.