So what exactly are you trying to achieve? Do you want an even mix of two movies (check out jit.xfade or use jit.op) or are you actually trying to do chromakeying? An example patch always helps us help you.
You need to be more specific if you want help. Check out Jitter Tutorials 8, 9, and 10 (in Max 4.6.x, that is). If that's not what you're looking for, a clear description is the most efficient path to help here.
I also have the same problem. I am using chromakey to attach different objects onto a movie. It is still fine when I try to output it to the pwindow, but when I output it to jit.window then the movie keep blinking. Could you please explain to me why? Thank you so much for your help!
By the way, may I ask you is it possible to use alpha channel to attach a jpg file to a movie? Thank you so much!