Dear Anand,
This happens as the standard Idoc FM for MATMAS calls a BDC for MM01/MM02 to make the changes in material master and while building the BDCDATA internal table for the BDC recording, system ignores the filed with no data.
To update field with space in target system, use the badi for batch processing for MM01/02 and add the field for processing when its blank/nodata.
Thanks,
Sanjay