We are also having the same problem!  We have never woried about it before as we where not using they system fully.  We were manually doing adjustments to inv because we were not suing WOs and we didn't have all our assem parts in.  How that we do have everything in the system (at least 90%)  we are really starting to watch our cost accounting.  
 
As you can guess,  This problem is causing us some major headaches!  I just printed 15 pages from SM-J-C!  Some of the stuff it want's to do isn't correct as we have parts that show the right amount in IN-A, but the transactions are off and the Serial for that part doesn't exist.
 
Please let us know anything you find out on this problem!
 
Right now I'm trying the IN-D  with rebuild to see if it makes any difference.
 
FYI,
 
We get issues on BKICMSTR, MTICMSTR, BKICLOC and INVTRX the issues are with POs, SO's, WIP, Location, WO's, Allocations.  Unfortunatly it says non of them will effect the GL.  However, adding items to BKICMSTR  Is going to throw my WIP and Raw material number off!