Note that this setting might slowdown the emulation for some systems. If this works to fix the core loading issues, then you should add this setting only in the respective systems' retroarch.cfg, i.e.
/opt/retropie/configs/msx/retroarch.cfg
/opt/retropie/configs/x68000/retroarch.cfg
while keeping the video_threaded="true" in the main configuration file to be applied to other systems.
Another thing you can try is to use the retroarch.cfg.rp-dist file instead and see if replacing the (long) retroarch.cfg with it would still make the bluemsx and px68k cores to crash.