Okay... I am now just totally 100% completely perplexed...
I enabled the Fetish version of the chat options window and logged in, played with it, and it was working how it was supposed to...
I logged out completely to the desktop, enabled the Fetish version of the main chat window, and logged in... I was sure by this point that it must be the chat window that was causing the problems... But when I got back in-game it was working as it was supposed to.
Now I'm just confused, I'm not sure what was going on originally. I have not made ANY changes to my files, except for renaming the files themselves (Adding DISABLE_) to the start of the file name to disable them.
The only thing I can think of is that after reverting back to the default UI version of the chat windows, and setting my channels the way I wanted them, when I went back to the Fetish version somehow something was "fixed" so that it was working the way it's intended.
I did test this by joining an entirely new chat channel, setting it to show only in one chat window, logging out and coming back and testing to see if it was going to the main chat window. It remained in the chat window where it was supposed to be, and wasn't showing up in the main chat.
One thing I just thought about is that I did not leave all of my channels and try to re-set them and see if they worked right. So no idea if maybe, somehow, because i was already in a few channels, the new channel I used to test this kept the same settings. *shrugs*
Oh and one last thing I remembered... I also switched to using the Basic Chat file that you include with the download. The default one that comes up when initially installing Fetish is bugged so that the chat overlaps where i type in my text entry.