Sorry For Late reply actuly I am out of touch with SCN due to project.
Actualy Bapi itself taking time. What we had done apply 261 with Bapi goods movement
and do only 101 with confirmation bapi. so ultimately we had generate two documents.
Just because of timing issue.
There is no problem with SAP or BAPI but as technically we can say for user's comfert we have to generate two documents.
Hope your issue sort out.
Regards,
Nayan Lad