Thanks for the info! Please see https://forums.boxcryptor.com/topic/subfolders-with-umlauts-aou-disappeared
Then you're experiencing this problem because the Final now supports UTF-8 which the Beta didn't. If a filename had non-ASCII characters in the Beta, these files will not show up in the Final.
If this is the case, the recommended way of upgrading from Beta to Final is:
1) Downgrade to BoxCryptor for Mac OS X Beta v0.9
1.1) You download it here: http://www.boxcryptor.com/download/BoxCryptor_v0.9_BETA_Lion_Installer.dmg
1.2) It is enough to install the BoxCryptor application (in "Customize")
1.3) As the beta expired at 01.07.2012, please adjust your system date to a date e.g. in June 2012 (System Preferences -> Date & Time -> Uncheck 'Set date and time automatically')
2) Move all contents of the BoxCryptor Volume to a temporary folder on your hard drive.
3) Correct your system date again.
4) Upgrade to BoxCryptor for Mac OS X v1.0 (you can simply install it over the Beta)
5) Move the contents of the temporary folder back to the BoxCryptor Volume