I would suggest you post the exact purchase order quantity and price, as well as the exact invoice value, best with a screenshot.
I haven't seen any bug fix for PP variances, so I think this issue must be caused by something else.
Since 0.12 is far above 0.01 absolute value a reduction of the tolerance to zero would actually just hide the real root cause.
SAP explains how the difference is calculated in KBA 1997545 - MIRO/MIR7: System will not issue pricing block according to your PP customization
But maybe the issue much simpler and it is just that your plant in your purchase order item does not belong to the company code in your OMR6 customizng