Same issue here. Only using one controller and four Riing Quad fans. Fans one, three and five always boot up on software start even though I only have fans plugged into one through four. Every time I have to turn off fan five and turn on fans two and four.
Software V 1.3.9 F, 3.0.3
AMD R9 5950x
AMD RX 6900 XT
ASUS TUF GAMING X570-PRO
Thermaltake Toughpower GF1 ARGB 850w 80+ Gold
GSkill Trident Z 4400 CL18 32gb 4x8gb RAM
I have since reverted back to 1.3.8 and it works fine. Loads up every time.