Hey Roman,
I've never seen this kind of issues. Most likely the Data Protector CRS has trouble reading the contents of lic.dat file or finding the correct IP address on the CM. I would recommend the following.
1. Upgrade to the current patch level (9.06)
2. Stop Data Protector services using omnisv stop
3. Remove lic.ctx from Omniback\tmp directory
4. Rename lic.dat to lic.dat_old and open it in Notepad
5. Start Data Protector services using omnisv start
6. Copy the one license string at a time from lic.dat_old and install them using the Data Protector GUI (Clients context)
7. This will generate a new lic.dat in the proper format
If the issue shows up again, run omnicc -password_info -debug 1-500 INFO.txt and omnicc -check_license -detail -debug 1-500 CHECK.txt. Are all licenses issued to the same IP address? If not, is the IP address still configured on the CM? It might help to disable IPv6 on the CM if it is not used. I had an issue once with mapped IPv4 addresses.
Regards,
Sebastian Koehler