I too am having the same issue. I have followed the steps you have suggested and even swapped the Y cable connector linking the two controllers.
I have 9 riing plus 12 fans, the the floe aio all connected to 2 controllers (5 on each). and I can only get one controller to be recognized at a time, either 1 or 2 depending which is connected to a certain end of the Y cable. see on either cord I use, only one end will register being connected to a controller. this is frustrating in itself.
I have a ryzen system
ryzen 7 1700x
asus rog crosshair vi extreme.
I'm a huge fan of these fans and thermaltake in general, but these fans are driving me nuts lately trying to get them all synchronized.