This really depends on what version of the beta you were using as a fairly recent version corrected an issue here. This version corrected the start time for dawn flats and uses civil twilight.
Sequence Generator Pro 4.3.0.1106 (BETA) is Released for Test - Releases - Main Sequence Software
In versions before 1106, it is possible that the time specified in the UI might not have matched the actual start time used by the sequencing engine. To answer your question tho… yes, that should be a start time for auto flats plus or minus 60 seconds.