Tried setting $relay_bot to the name of the second org bot?
That variable is supposed to fix your problem.

$guild_relay_target = $this -> bot -> get_setting("Botname");

is what I have in my guildrelay file - using the beta version and there's no $relay_bot variable anywhere so I changed the name.
Did I invert where to put the Botname or?

EDIT: I tryed to put the botname into the $other_bots variable in the conf file, it works but as I thought this stops the relay between org chats - since the point of that variable is to prevent flood from raid bot to guild chat if I got it right.

I'll try and dig into the original file and see what could be different, although as I posted on my previous answer when you add the name of relay bot into the $other_bot variable they dont display anymore when doing the online function - cant use it since it wont relay a word anymore but could be a hint.

Uhm - I mean the $relay_bot variable in the Rooster_GUILD.php. It's only used in the loop to build the buddy list of the bots.

Just edit the line to $relay_bot = "whateverthenameoftheotherbotis"

My bad, I didn't read threw the whole code and thought $relay_bot would go and check into the conf file for the name of the relay bot itself.
I cant test it right now since I'm having a few other issues to fix but that should solve it.

Thanks a lot for you answer and your time Alreadythere.