After installing Juno it seems not possible to middle click paste between certain programs anymore. Within the same program it works just normal. Also the option in the Settings app does not effect this behavior at all.
It's normal Juno behavior to copy/paste with ctrl+c - ctrl+v, even from terminal. Try elementary tweaks. There you have the ability to change 'natural' copy/paste. Just disable it and you have middle click working again. Maybe you need to reboot for changes to take effect.
There was an issue in Terminal that prevented it from working properly with the system-wide setting. That has since been resolved.
Now you should be able to head to System Settings → Mouse & Touchpad → Clicking and toggle the Middle-click paste option for it to work system-wide.