Please check the material master Purchasing view for the field MPN profile.
If you have "unrestricted MPN" profile active, it could explain the issue.
With unrestricted MPN profile you can choose to buy a specific manufacturer part OR order using the IM material number and specify the manufacturer part at time of GR.
Of course from a procurement standpoint, procuring the specific MPN part and the generic IM part are two different items - in one case you are telling exactly which item you want to buy and in the other you don't know yet.
I would expect SAP to create the PO with 2 items: 1 for the MPN part and the other for the I'm part.
Also can you paste a screenshot of where on the PR you see the MPN part number field?