Hi Suresh,
As per Standard SAP, the return activities are determined from customising corresponding to the return reason and you have an option to override them in event 265.After that, once the return activity is posted in SAP, eitherways, through 296/299, then include program,LFKR2F01, does the rest.
To Start with, are you getting any errors in SLG1 application logs for the scenarios, where the payment method is not getting deleted during the returns processing,
Morever, can you check whether the items for which the return activities are not getting triggered, whether there is a return reason populated for these items in DFKKRP.
Check the list of CA's for which you are getting this issue, to find any similarity b/w them
Hope it helps..
Thanks,
Amlan