Hi,
Just to say: me too, using up-to-date package:
Linux cloud 3.2.0-77-generic #112-Ubuntu SMP Tue Feb 10 15:22:22 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=12.04
DISTRIB_CODENAME=precise
DISTRIB_DESCRIPTION="Ubuntu 12.04.5 LTS"
I am using openfire_3.9.3_all.deb, MySQL database with LDAP auth backend and I get exactly the same result as Samuli got 8 years ago!!!! Openfire user does have R/W permission to keystore, truststore, security folder, etc. Whenever I restart openfire: the self-signed (openfire created) certs are gone.
Should/could someone (me?) file a bug somewhere?