Hi Theodoros,
Good to hear your issue is resolved!
When we create the Drive Mapping Boot disk, all we do is populate these values in the system.ini file. It is similar to creating it manually and editing it. So it is difficult for me to think what the reason is.
It could be the way your policies are setup. I still think it is related to NTLM, but when you use a Domain account, server need to authenticate the user from the Domain. May be it is expecting a higher version of NTLM in that case. But if it is a workgroup machine, server could authenticate locally.
I'm not sure if this answers your question, but that's what comes to my mind.
Krish