Hi Priyanka,
It may happen that after the Security upgrade there are some more authorization checks, which have been introduced in the standard program which is taking up the time.
If you put a trace on, you get the authorization objects, which are getting hit with the execution of the program.
Also check if you are running some other mass job or not in parallel to the payment job, it will also have an impact on the performance of the job.
Hope it helps
Thanks,
Amlan