Hi Matt,
There are no hard limits to the number of flow trackers. As long as your memory and cpu utilization are under control you can have any number of them. You can check this from Admin > System Perf
Most likely your problem is due to the email sending service not getting started. Please go to Admin > Start Stop Tasks > Start Email Notification Service. This should start it. At the moment this service is not started automatically on reboot, you need to start manually from the UI. We will fix this in the next release.
Regards,