So the question is if there are some restrictions in freeradius when it will stop to communicate with AD in some special cases ?
No. This is not a FreeRADIUS issue, this is a Samba issue. NTLM Auth is not part of FreeRADIUS, FreeRADIUS merely calls the ntlm_auth executable to proxy MSCHAPv2 data to an Active Directory server. Or to perform simple authentication with a username and plaintext password.
Get ntlm_auth working reliably, then try and use it with FreeRADIUS.