I can't reproduce it. This is my folder structure:
/gentest/
/gentest/_LLBLGen Project/
/gentest/MyTypeConverters
/gentest/out
the batch file (get.bat), which is located in the root of this structure looks like:
cligenerator.exe "_LLBLGen Project\NW.LLBL.MSSQL.Adapter.v31.llblgenproj" .\out\ 1 outputLog.txt
Some fields uses my own TypeConverters located in the corresponding folder. The AdditionalTypeConverterFolder property of the LLBLGen project file is: ...\MyTypeConverters. The CliGenerator works fine, the loading of the .llblgenproj file in the Designer is fine as well.
Do you have a scenario different than mine to reproduce your issue?