what version did you had before you installed pkg_jem_v3.0.4 ?
@lobebe
the reason for asking is that any JEM 1.9 or JEM 2.0.x versions are not intended to be installed within Joomla 3.
so if you had that then you might have problems.
IF you installed JEM 2.1.0 then be aware that aldo it can be installed within Joomla 3 it can give problems when you are installing JEM3 on top of it. This as the link between those two versions is missing at the moment, it will be created but that will be next year.