General reply for this thread - I posted this in another one but this thread is now higher up in the ranking so I think it is worth repeating :)
You are doing nothing wrong per se; upgrading directly from MINIX 3.3.0 to the most recent MINIX3 source has simply become impossible. It is only possible by going through an undefined number of intermediate steps, which is more painful than it's worth. Instead, we advise anyone who wants to try the most recent MINIX3 source to start with the most recent release candidate: MINIX 3.4.0rc2, for which the ISO can be obtained from:
http://download.minix3.org/iso/snapshot/Starting from 3.4.0rc2, it is possible to upgrade to the most recent source in one go. My apologies for the inconvenience.
Regards,
David