@briansusername, you might benefit from doing a catch cup test to measure how much water is being applied to your zones. Here’s a great white paper written on the best practices of how to conduct a catch cup test by the Center for Irrigation Technology.
Just curious, is this occurring multiple times a day? I wouldn’t think that a quick manual run once a week will throw off your Flex schedule much, but happy to review your account for you if you’d like. Just email our support team [support@rachio.com] and reference this post.
I have a few ideas on ways to fix this for short durations, but it will take some testing before we can make any major system changes. Pending the test results, I’ll post an update here in a few weeks.