On the download page, they have not removed v1.3.8 - that should be a HUGE clue on what to do!
I had the same problem. New Riing Trio 12 with controller. Installed it, loaded the software (1.3.9) and I thought my controller was bad. Any fan plugged into 1 worked. Any fan plugged into 3 mostly worked, but I would get the Exclamation Point of Doom on 5 - even with nothing plugged into it - along with the Controller 1 warning splash. I put a fan in spot 5 and sometimes it would work, sometimes it would error, sometimes I needed to reboot - - - a freakin nightmare. No combination seemed to work.
I uninstalled Thermaltake Tool 1.0 and TT RGB Plus 1.3.9, then deleted the folder "C:\Program Files\Tt", then deleted the folder "C:\Users\<Your Name Here>\Roaming\Tt". Rebooted, installed 1.3.8, and everything worked the first time, just like you'd expect.
I wasted about 6 hours on this and found the solution in another thread. It was a hard forehead smack to see the solution - it was right in front of me the whole time. Never saw it. Nice hardware, but without the corresponding software working it doesn't matter. The whole package winds up being bad.