Hi,
When you get this error message: "Time out while booting. Press OK to finish, you will have to manually upgrade the board". This trick worked for me:
1) Unplug your board.
2) Click on Upgrade & Erase.
3) Plug back your board.
4) It will update but block while the "Remove settings from the board" process is starting ...
5) You unplug again and plug it back.
The Upgrade will be successful, just unplug and plug your USB cable back before it shows the red error message about the timing-out.