I think that Todd's suggestion is probably what will solve the 200 job limit. However there are a few other throttles you should look at:
DAGMAN_MAX_SUBMITS_PER_INTERVAL defines how many jobs get submitted during each submit cycle. The default is 5 which is pretty low. You could try increasing that.
MAX_RUNNING_SCHEDULER_JOBS_PER_OWNER might also be a factor. Are your cron jobs all running under the same user? I don't think this is the problem here, but keep it in mind if previous suggestions don't work.