So I did some more digging around wherever I could to find the issue I was having.. So I took a look at my router configuration, which included some system logs and routing tables.
While all my 2001:* addresses were listed there, so were some 2605:* addresses. So I got a little excited and had to make sure. Disabled my tunnel completely, changed my router settings to "native", and sure enough.. I now have native IPv6!
I wonder if that had anything to do with the double addresses issue I had, since my router was set to use the prefix 2001:* could it be possible that since I had a native address coming in also, that my router may have tacked on the prefix and left the rest? I'm not sure.
But after getting rid of the tunnel and going with native, I now only have one v6 address listed.. so the issue may have fixed itself now.
Finally, after verifying that bbs.pharcyde.org (both ports 24554 and 24555) answer with a 2605:a000:140d:41cd prefix, please change both of my listings to Native please, and my ISP is Time Warner Cable (TWC for short).
