Root cause was found. 
Its MR11 - GR/IR account maintenance. There was an enhancement during MR11 posting - not to post to inventory account, but to post to some other adjustment account. Because of this, whenever business used to clear GR/IR account, it used to change the MM valuation, but it was not hitting the inventory account causing the differences.
How did we find the issue - we fetched all the entries from table BSEG for transaction KTOSL = BSX and G/L account HKONT # inventory account and analyzed the records.
We have now removed that enhancement.
Thanks for the help.