Hi
There could be various reasons for this. Check below SAP notes, specially the first KBA:
1641525 - First steps in case of BOP performance issues - APO BOP
1834083 - Performance problem when running BOP
1976896 - Performance improvement in backorder processing
2096776 - Performance improvement for database selection /sapapo/ordadm_i
2224542 - BOP: Performance problem when saving confirmations
1689510 - Increased runtime in BOP due to "Delete Switch"
You can also check more notes in SAP support.
Regards
Rahul