According to our testing, upgrading from one high-end GPU to two high-end GPUs will speed up processing only for projects with 4 or more cameras. For projects recorded with 1 or 2 Kinects, dual-GPU setup may actually result in slowdown.
This does not explain the slowdown from 0.9 seconds per frame to 2.4, though. In your case, it looks like there is a problem with configuration of video cards. DirectX 9 does not have tools for proper detection of actual GPUs in the system, so you have to disable SLI and follow this guide for enabling multi-GPU processing:
http://wiki.ipisoft.com/Multiple_GPUsMaybe the GPU with two 21" monitors is detected as two GPUs. In that case, disconnecting one of 21" monitors may help.