This is a known limitation of the current rain delay (skip) mechanism used. Unfortunately it puts the controller into a rain delay for other schedules as well if there was any overlap of the non rain skip enabled schedules.
We've made a small adjustment to make this less brute force and released this fix tonight.
Schedule A starts at 6:00am and ends at 8:00am
Schedule B starts at 7:00am and ends at 9:00am
If schedule A was skipped unfortunately it would have skipped schedule B since we were setting the rain delay from when we detected the rain delay ~ 5:10am (about 50 minutes before) to the end of schedule A. So, the rain delay was set from 5:10am - 8:00am. This would catch any other schedules and skip them.
Our slight fix to this is we are only setting the rain delay now from when we detected the skip to about 5 minutes after the start of the skipped schedule. This should help you with setting schedules much closer together that are not meant for rain skip. So, in the previous example the new rain delay would be from 5:10am - 6:05am.
As long as you set your schedules that you don't want affected by rain skip slightly ahead (I'd say 10 minutes for good measure) then they will always run as normal, with no rain skip.
We understand this is less than ideal and somewhat confusing, but it is how the current system is implemented.
We are working towards a much better permanent solution (only skipping the exact schedule).
Please let us know if you have any other questions.