The issue I was running into was that I had the #LINKTO function in quotes.
The easiest explanation I can provide is - It's basically a tool that allows you to tell a side story or add another scene and then loop back into an existing storyline.
As simple as I can explain (for my own benefit I had to break it down like this):
Go to the thread you want to branch off from
Create a new thread at the end of it (called NOTHING - or some name easy to remember)
Save the thread
Look in the thread list for the already existing thread ID number you want to link back to
Edit the new thread called NOTHING
Past the answer of the thread you want to link to in the "Answer" field
In the body, just type #LINKTO and the thread number right after it. Like: #LINKTO 169892
Save the thread.
Now when you go back to the previous thread, you should see the option to choose a path to the existing storyline
Hope that helps.