FSSO wont collect correct groups

I have this setup: a DC + FortiGate Firewall in one branch and another DC + FortiGate in another branch.

Branch #1 works ok. Using FSSO agent I can collect domain groups and filter web traffic (All is fine)

Branch #2 There is a FSSO installed on DC with exact same config as Branch#1 and group filter is set to filter just couple groups. On FortiGate Security Fabric, connector is up and running but it wont pull filtered groups. It pulls lots of other groups from other OU-s. 

When I connect mentioned Branch#2 FortiGate to Branch#1 DC then groups come up as designed.

There is no DC Collector agent installed on Branch#2 (It was there but I removed it).

Any ideas?

P.S. I don't want to use LDAP.