Am 07.07.2014 um 17:15 schrieb Karlos Jelez <otrsfan@gmail.com>:

My 2 OTRS instances are separated, working on their own directory (/otrs1 and /otrs2) with separated Config.pm, Kernel.pm and Defaults.pm files, separated scripts into httpd.conf Apache config and separated cronjobs.

I did try with 1 and with 2 MySql users to each OTRS instance, with 1 and with 2 operating system users, but it did not solve the problem.

I think the problem is in how I am using apache2-perl-startup.pl script: Each script was modified to point to a different directory; I dont know

Problem is that you are using mod_perl for both instances. Together with DBD (afair) this leads to only one DB connection for both. Try to either disable mod_perl for one instance (you may use fastcgi instead) or find a configuration that allows for two separate perl environments with mod_perl.