I know I have encountered this issue before but for the life of me cannot recall what I did to fix it.
After re-installing version 4.106 of TeraTerm with LogMeTT, restoring my list of hosts (.LTT file) and confirming I can manually connect to a destination in teraterm, LogMeTT goes wierd :). On my original system, when you "Run Branch" to execute the login script, a copy of the existing TERATERM.INI file is copied to the %AppData% temp path and TeraTerm uses that.
Since re-installing, the copy of TERATERM.INI is not happening. Instead, the temp file generated, contains some random character and nothing else. Did I miss a checkbox someplace in LogMeTT?
Installing LogMeTT as a user instead of admin seems to have corrected this oddity.