The Minion self updater can't preform these updates, sadly. It would have taken too long to roll out an update to old minion so that you could update to Minion 3. The reason for this is that there were a ton if internal path changes and library changes. We also updated the Java virtual machine's jre to the latest version available.
Thats why I put a big download button in the update notice notes on the old minion.
Future updates to Minion 3 will work like normal and not require a re-install.
My log says windows 10 when I run Minion. Are you running Windows Home or Pro?