Like Alge said, it sounds like your macros and we can't really troubleshoot unless you post those macros. You're talking about replacing macros with just plain spells. We need to see those macros because from the way you describe it, it should simply be /cast whatever, but from the problems you're having, it's castsequences that are locking up somewhere - probably centered around Chaos Bolt because Chaos Bolt has a resource requirement.

It's my understanding that ISBoxer doesn't wait around for steps? IE, Press = try to cast step 1, release = try to cast step 2, press try to cast step 3 etc. If that's the case, then it shouldn't get "stuck" and prevent the rest of the steps from processing, it should simply ignore what it can't do and come back to it next time around.