My bad, I haven't tried too much since then :( To be honest, I had other problems as well then (not only vice, I mean), and it seems all is about Wayland-related topic, so maybe Linux distros using Wayland and running vice over XWayland then (?) are affected. Anyway, I switched back to X.Org from Wayland, it seems it has got too much problems with many software including vice. Since then I haven't got a single problem. Now, upgraded to Ubuntu 18.04 LTS, and still no problem, not using Wayland though...
Vice emulators (all of them) crashes on Ubuntu 17.10 on startup
IstvanV: debugger window memory area pointed by...
Support of 254 tracks
IstvanV: debugger window hex dump: reversed ord...
IstvanV: opcode ED 71 mod
Adding .gitignore files
IstvanV: Z80 'random register values on reset' fix