I have tested the upgrade on three pc and here you are the problems!
1) the version on the "About" window is wrong: 1.6.400.0 but the version on the .exe is "correct"
2) the user.config file is saved on a subfolder of %localappdata% named 1.6.400.0 instead of the correct 1.6.400.53
3) on the changelog is written "Changed: Settings from 1.5 versions are now preserved when upgrading to 1.6" but it's not true, I had to manually save a copy of user.config and restore it after having closed the 'First Time Wizard'. The 1.5 uninstall is deleting everything!!
4) the initial setup is creating the wrong autostart key into the registry, you have to manaully enable the option 'Start with Windows' and then you have TWO!
Here you are the entries, the v1.5; the v1.6 wrong; the v1.6 correct (after having deleted manually the previous two entries)
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run] v1.5
"BoxCryptor"="\"C:\\Program Files\\BoxCryptor\\BoxCryptor.exe\""
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run] v1.6 "wrong"
"BoxcryptorClassic.exe"="\"C:\\Program Files\\Boxcryptor Classic\\BoxcryptorClassic.exe\""
"Boxcryptor Classic"="\"C:\\Program Files\\Boxcryptor Classic\\BoxcryptorClassic.exe\""
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run] v1.6 "correct"
"Boxcryptor Classic"="\"C:\\Program Files\\Boxcryptor Classic\\BoxcryptorClassic.exe\""