Hi Gavin,
No BADI (including RUNLOGIC) has control over these parameters. BPC writes 2 files in UJFS when a script is executed: header file and detail file. Header file has a time stamp that is a reference to detail file. When the header file is written BPC assumes that script will start at same second. I saw a difference in 1 sec between these 2 time stamps, but I never saw 12 secs like you have.
Can you please try changing you DEBUG parameter in START_BADI (default is OFF).
Thank you,
Gersh