FYI for anyone running in to the same issue:
This issue was solved by using a more recent firmware recovery image. Anything older than 7.0.3 will appareantly not repartition the harddrive automatically according to the experts 🙂.
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Dustin 160
I recommend contacting UltiMaker Support directly about this issue.
UltiMaker does not offer official support via community posts.
But it sounds like you might need to preform a firmware recovery.
You can contact support directly here: https://support.makerbot.com/s/contactsupport
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