I can't seem to figure out how to stop joining the same channels everytime I connect, either when opening program for the first time or reconnecting. I have nothing in my perform list and everything relating to rejoining under IRC options is unchecked. I want to stop joining this one channel because no one uses it anymore and it's pointless to be there.

Do you have the channel listed in your Favorites folder? It may have the "Join on Connect" option enabled.

Maybe you have them added to ajoin list via nickserv commands.Hope this helps
Try typing /ns ajoin del #chan

Nope, it's not in my favourites. I don't even use that list.

You may have a script that is joining channels, or the network itself is forcing you into a specific channel. If the network forces you into a channel, there's nothing you can do about it. If it's a script, you just need to find out what script.