For anyone who is having this issue, there is a solution.
The solution is simple, first go to your keybindings and add a binding called "Fullscreen Fix" or whatever you want to call it. Next set the keybinding to F11 and make it execute the following command: wmctrl -r :ACTIVE: -b toggle,fullscreen
Now reboot your system and start up Minecraft. It will now be fullscreened at the resolution of the monitor it is on (so the issue is solved)!
Timofey Cvetkov
For anyone who is having this issue, there is a solution.
The solution is simple, first go to your keybindings and add a binding called "Fullscreen Fix" or whatever you want to call it. Next set the keybinding to F11 and make it execute the following command: wmctrl -r :ACTIVE: -b toggle,fullscreen
Now reboot your system and start up Minecraft. It will now be fullscreened at the resolution of the monitor it is on (so the issue is solved)!