Sorry, I'm not following.
You have a single DMX channel mapped to all of your layers transition time control, right?
So when you turn that channel up, it turns up the transition time for all of your layers, right?
Is it also turning other parameters up as well? Is that channel mapped to something else or just those transition time controls?
If you open up the applications preference window. then go to DMX, there is a > right arrow at the top right. Use that to help identify what DMX signals the program is receiving. Make sure you're not sending other DMX channels as well.