Is it possible to use the 'screen' command to work with files on an encrypted home directory?
Solution 1:
There is a file named /home/.ecryptfs/$USER/.ecryptfs/auto-umount which is used as a flag for umounting the encrypted partition whenever you don't have a login shell anymore.
You might want to remove this, or (untested!) try to create another session within screen (eg run sudo login and login with the same user, within screen, this should keep the number of login-shells above zero).
EDIT: ecryptfs use who to count the number of logins. If you feel like troubleshooting...