Three things come to mind:
1) You played Minecraft Pi Edition earlier which implies you configured the legacy driver. Did you remember to reenable the full OpenGL driver with KMS before switching back to Java Edition? Run
sudo raspi-config and reboot, then check your framerate with
2) You could actually be running out of memory depending on the size of the world and other stuff running. Run
htop while loading to check.
3) Full OpenGL might not be fully supported on Ubuntu MATE to begin with because it uses an older kernel (4.4). Unfortunately I can't test this now because I'm using the 64-bit kernel, but let us know what happens after you've tried the above.