Hi
Sorry for my late reply. I was travelling and then landed in a Go Live situation.
Which kind of transaction is this? SD Billing ? PGI or ??
Usually you dont have to do anything to populate the Qty.. If the Field Status Group (GL and Posting Key) allows the Quantity Field - It should populate automatically. So check this aspect
If it is PGI, make sure you dont do PGI from VL01N. Do it from VL02N
Though not needed, but see if the activation of "Record Qty" in Cost Element Master helps you
If nothing works, I would debug the Good and Bad cases side by side, to find out why one document is not getting it.
Ajay M