Hi Ken,
As far as i'm aware, this is no bug.
This can happen for multiple reasons: you ran 'itmcmd config' and the Putty session got interrupted for whatever reason, you are updating the config files using multiple ways (itmcmd config, via TEPS, manually, ...) at the same time, you are entering some unexpected characters (like a backspace) in the 'itmcmd config' prompts, or you have some codepage that is not supported.
I suggest you raise a support case to get this investigated.