Jawahar,
Where are you running the Promotion Manager Tool? You need run the Promotion Manager tool from the BI 4.1 w/ SP5 and do a pull from BI 4.0 w/ SP5. This should NOT cause any issues, I have customer currently running BI 4.0 w/ SP4 and BI 4.1 w/ SP5 and they perform pulls all the time without any issues.
Regards,
Ajay