Quartus II on Linux: Adding custom JTAG devices to programmer

I've got a board which features an EP3C25 and another device on the same JTAG chain, and on Linux I can't save a .cdf for this board, because the programmer doesn't recognise the other device.

I click "Add Device" and create a custom definition for this device, and then I can save the .cdf file.

Here's the problem: On windows, next time I run Quartus and open the programmer it remembers my custom definition and everything works as it should. On Linux the custom definition seems to be forgotten, and I have to do the Add Device thing again every session.

Any ideas how to solve this?