PIM added entries to /etc/pam.conf which caused certain functions, e.g. some cron jobs, to fail.
A 3rd party product made entries to /etc/pam.conf which the PIM install detected so entered it's own entres.
/etc/pam.conf should not really be used on later versions of unix and linux which use /etc/pam.d, and PIM has to take into account /etc/pam.conf because some versions of unix still use it.
You should also expect some pam configuration changes to be necessary if other products also make changes.
If you are automating the install, a workaround would be to do something like the following in a script:
mv /etc/pam.conf /etc/pam.conf
mv /etc/pam.conf.pim_install /etc/pam.conf