Ideally live restaurants would not be using clear db transactions. But you should Disable virtual work periods, Stop work period, clear transactions, start a work period, End a work period then enable virtual work periods.
It has to do with the fact that it only designates a start time… it uses last ticket before that start time as the end time. You must have one full work period before you can enable VWP. IF there is a WP that is already closed after the designated start time for VWP then it will not auto start.
Virtual Work Periods is just one continuous work period with start time for reporting. When you manually end a work period it will auto start work period at next days start time as long as it knows there was a valid end before that point.