I'm sure that Laurie will ask for more details, but kind of problems are you having with JT Alert's processing time? I monitor 8 bands simultaneously and, even when conditions allow for 30+ decodes per band on multiple bands, I don't experience anything that I would consider abnormal. This is on an i7 Win7 64 Pro system with 8GB of RAM and an SSD.
One thing that I have noticed is that my friends that use WSJT-X and JT Alert have experienced differences in performance based on which security suite they're using. One friend had to go to great length to get NAV to "trust" everything that WSJT-X / JT Alert interacted with because of very high CPU utilization on every decode cycle and ultimately reduced a visible slow-down to virtually nothing.
Hope this helps.
Mike - N8MSA