sadly i get dependancy problems on linux trying to use 3.9 so had to give up, i'll just have to wait for the flatpak version to eventually update 1 day which will include all the right stuff needed without breaking my system.
what exactly does the crt need in 3.9 that isnt available in 3.8?
Basically it requires the MD2 cartridge format support, that is available only from 3.9 r45695 and on. If you have problems with running VICE I suggest you to ask to the VICE development team how to solve your problem.