I do not believe that Linux has Third Party import tools. I would look at your installation logs and see if the Third party conversion tools were installed.
We too have both Windos and Linux users and I routinely make conversions from Altium/Protel -> Windos -> THEN open it in Linux. I've been very successful, but you have to use the right version of the Mentor tools. The import utilities in some versions work better than others.....and CDB vs: Netlist makes a difference too.