Not sure what might have caused this, unless lots of rain delays are frequent in your area.
I see you are now only using custom watering, this should be pretty reliable unless your rain delay settings are still to sensitive.
You can fine tune when automatic rain delays will be set. Go to Settings – Devices – select your device & scroll down to Weather Adjustments. From there you can set the percent and amount of rain forecast before a rain delay is set. If you want it to be more sensitive lower the values and if you want it less sensitive increase the values.
I have also pushed an update to your timer, it was a few versions behind.
Let us know if you have any more issues.