Thanks so much for getting back to me so quickly!
For the already launched Tundra module, Bay 1 is Materialkits and Bay 2 is SpecializedParts. Bay 3 SHOULD be Machinery but always seems to switch instantly to MaterialKits.
The setup is as follows for the already launched Tundra module when I change it in EVA:
Bay 1: MaterialKits --> SpecialisedParts
Bay 2: SpecialisedParts --> Machinery
Bay 3: Machinery --> SpecializedParts
But when I change back to the craft, Bay 3 is changed back to Machinery
However as per your queries, I checked the VAB version of this craft and a newly launched version. In VAB, the same craft accepts the MaterialKits/SP/Machinery combo that I wanted. Additionally when I launch the same craft, the new version seems to accept Machinery as the 3rd bay once loaded onto the launchpad.
Is there a chance my latest Tundra module is just bugged out?