There is a bug with IGT when you start a run from a quick restart. The timer seems to count the time from when you hit quick restart, to before it starts to generate the first floor. It adds 2-3 seconds to a run, to avoid this start a run from the breach.

Been known for a while but thanks for the reminder for any new people that show up.

I assumed as much, but it took a while for me to notice so thought writing this might save someone learning the hard way.