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when I configure the password generator to custom settings and save the settings to a profile name of my choice, this profile is not available when keepass gets restarted.
I guess, the path to the profile directory does not exist and the profile is not stored correctly.
Please check - its ubuntu 13.04 (but was also the case in earlier versions).
The custom password generator profiles are saved in the <UserProfiles> section of the active KeePass.config.xml. If they are not being saved then make sure that the config file can be written to. This file should display a Date Modified corresponding to the time you last exited KeePass.
The contents of keepass.config.xml can be viewed with a text editor.
this config file is status rw/rw/r or 664 within $HOME/.config/KeePass/
So path exists (if the correct one) and settings should be correct.