We are importing all versions of documents, but the Migration tool keeps resetting the library to capture only Major versions (not Major + Minor versions)
The current version of SharePoint does not allow us to explicitly set version numbers as we migrate. So if I attempted to migrate versions 1.0, 2.0, 2.1 and 3.0 it would have ended up as 1.0, 2.0, 3.0 and 4.0. Similarly, if my Domino.Doc library had pruned old versions and we now had only 3.0 and 4.0, that would have become 1.0 and 2.0 in SharePoint. We are trying to convince the SharePoint product team to address this limitation for SharePoint 14, but for now keep in mind that this feature works best if you select all published versions in your query. A workaround when you can’t do that is to explicitly migrate the “{VersionNumber}” field to an additional SharePoint meta-data field so you will always have that as a reference.
Please refer to the whole article explaining version migration here