MPP installation issue in Aras Innovator11SP12 - part classification structure

We had a modified part classification structure (over and above the default set of Assembly, Component, Software and Material, I had introduced extra subclasses for products/machines/ tooling, to help the designers segregate the different kinds of part that we use in our company. However since MPP installation requires the default class tree, I eliminated the customization's and restored back to the default 4 types without sub-classes. Even then the MPP installation fails. In a test server however, even though there were 2 extra part types added, it still managed to install the MPP application. I checked the validatePartStructure log in the scripts folder of the MPP installation (in ProgramData/Aras/ArasUpdate/MPP....) the class ids of the part types match identically to the one in the test server where MPP installed. In spite of it, it says part customization's observed and therefore cannot install MPP. Can anybody help with how to resolve this? We really need the MPP application to set up our MBOM.
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