If your command that has the pause does not have the, 'allow other commands to execute while this one is running' it will block other commands from running until it is finished (and cancel them if you have the Options > System Advanced > 'Cancel Blocked Commands' option selected). Otherwise, a paused command runs in it's own space (thread) and does not prevent anything else from running.
You'll want to test out your commands in an empty profile with no plugins to make sure something else isn't interfering.