When jobs are running, Control-M is merely waiting in the background waiting for them to finish. It does not interfere with the run in any way. If it runs at the command prompt normally, it will run through Control-M.
What I've usually seen that causes this is either the machine is misconfigured, the machine is overloaded, or the environment is different in some aspect from when they run it "manually" vs. batch. You have to compare apples to apples -- and that is the tricky part sometimes.
My first question would be, if I was researching this, why are you running 1,200 commands in a script file? That defeats the purpose of Control-M in more ways than I can possibly type out here. I'm not saying create a 1,200 "job" workflow, but they need to be breaking those down into more manageable tasks. Otherwise, if you fail on command 1,199 you are going to have to restart all the way from the beginning -- that's not going processing logic.