I run 2 instances of cgminers because I have two cards one which performs better for SHA256 and the other performs better for the SCRYPT algorithm.
Effectively increased my hash rate by 10 percent doing this.
The only problem is when you use --auto-fan and (presumably) --auto-gpu
The nuisance is that cgminer version 2.4.1 is trying to control the fans of the GPU card that is turned OFF which causes unwanted rapid oscillations in fan speed as 2 cgminers are trying to control the fan of a single card.
To solve that, you need to go in G(PU)/C(hange)/#/A(uto)/F(an) where # is the number of the GPU card that is set to OFF in a specific instance of the cgminer.
This will prevent cgminer from accessing the fans of the card that is turned off.