This is not a known issue with Tunnelblick.
It sounds like something is treating the security code as a number instead of a string. Thinking it is a number, it drops the leading zero because the number 0123 is equal to the number 123. The string 0123 is not equal to the string 123.
Tunnelblick always treats usernames, passwords, and security codes as strings, not as numbers.
It is probably a bug in the VPN server. The server (or some security software it is using for the secret code) calculates the security code as a number (it must, if it is a TOTP), but it isn't properly converting that code from a number to a string – it is losing the leading zero.
You need to contact your VPN service provider. That is the organization which gave you your configuration files, and perhaps a username and password, and to which you are probably paying a fee for VPN service. For more information, please see Getting VPN Service.