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Finally solved it. Somehow from the installation documentation I got the idea to add a port from br-int to internal network just like br-ex is.

So the solution was to remove the port and deconfigure ip from br-int and now it seems to work.

The key to solving this was that the internal vlan communication of the hosts was leaked to the physical network as it should be tunneled with GRE. After scanning through the openflow rules (not recommended reading for anyone) I finally figured out how the networking shoud work. The GRE tunnels are configured with remote_ip=<destination> which will send them with correct interface and need not be connected via openvswich to physical interface.