I am just going by the list that the manufacturer QVL List states what is compatible. According to the list, your RAM is compatible in 2 DIMM slots.
Maybe you should open a MSI Support ticket and let them know that they need to update the QVL list concerning DIMM slots being compatible, at least with the APUs, and also to see what they recommend to fix your issue or what is causing it.
Another User in the past had a similar issue. He mentioned the RAM worked only in 2 DIMM slots and not 4 DIMM slots. So I showed him the QVL list showing his RAM is compatible on 2 DIMMS and not 4 DIMMS.