Hi Till! Than you for reply.
The problem is that NO SENSE to look for the /etc/shadow because even for the same password the encrypted string differs (it adds randomness during the encryption). So the exactness fails always!
After modifications to /etc/shadow does not work the standard linux authentication, gives the password error for some users.
I saw ispconfig doesn't use passwd/usermod/useradd functions to modify the user data (name/password/shell), it implements adhoc functions in php. Is there any restrictions, some default action that the php perfrom, when for example the password is shorter then some number characters??