Could you please provide more information as to what exactly isn’t working? Could you possibly provide some screenshots while making sure that no sensitive information, such as public IP addresses or MAC addresses, is visible?
What firmware were you running before the upgrade?
A similar issue has been discussed on this particular thread: L2TP to PC RUTX50
Where a user has set up L2TP over IPSec, and the tunnels weren’t going up. The fix was to upgrade to the firmware version 7.19. Downloads can be found here: RUTXR1 Firmware Downloads - Teltonika Networks Wiki