1. As for Lotus client, I have installed it at the server the same day I have posted this problem. I mean, the problem appeared before I installed Lotus client and I have done it in order to try if I am able to access ServerB/Acme2 from that machine. And everything was OK with that..
2. BES and Lotus have been restarted a lot of times since problem appeared. Every time I change something I restart both Domino and BES.
3. As for the hidden views $CrossCertByName and $CrossCertByRoot .. I indexed them on both servers. I am sorry, I did not mention it and a bunch of other things I tried in order to fix this weird problem but nothing helps.
Thanks for keep trying to help me guys!