Hi Ryosuke,
When we have the shift sequence assigned to work center then while scheduling system use the time from shift sequence it overwrite standard available capacity.
Check both the formulas for calculating the execution time in the work center as well as the standard values used in the routing. Also check "Scheduling allowing for breaks" is active in system in OPU5.
For lead time scheduling you need to use have MRP control parameter Scheduling as 2 Lead Time Scheduling and Capacity Planning.
Also refer consulting notes 152319 - Consulting: Scheduling of planned order for routing
Regards,
R.Brahmankar