Whenever ELectricSentry runs a build, that build includes all changes since the last successful sentry build. So if you had two check-ins during the quiet time, both should be included in the next build.
When checking for the quiet time, Sentry asks the ECSCM driver to report the time of the most recent change that affects the defined portion of the depot. It waits for the difference between that time and now to be at least the quiet time. So, run#3 will trigger after the quiet time delay has elapsed starting from the time of the last check-in. If a check-in happens right after the run#2 starts, then run#3 may trigger immediately after run#2 finishes if run#2 took longer than the quiet time to complete. Sentry will not schedule more than one build at a time for a given configuration.