After upgrade to DB 12c HR retropay by element request takes long time

Dear Gurus

we have an Oracle EBS instance version 11i (11.5.10.2), on Oracle database 10g R2. we are in the process to upgrade it to R12, but for now we only want to upgrade the database to 12c.

in the upgrade test I finished interoperability notes, and everything looks fine. while testing we found some slowness in the system but the issue was most obvious with Retropay By element request in HRMS module. the request used to take about 3 minutes on the old system, now it's taking about 12 minutes !!! , I used express enterprise manager to generate a new explain plan for the query which said it should give 68% improvement but until now we are still on the 12 minutes. I have sufficient memory and CPU on the system. so what can cause such