I have few questions to you,
1) Have you set up an serial number in EPDM to generate document number ? or Entering the Document number manually into the Data Card ?
2) Have you mapped the Data Card Variables to Configuration Specific tab in custom properties of the file ?
3) Are you using Items in EPDM ? Which version of EPDM are you using ?
If you can answer this question i would be able to help.
This is a known issue. SPR exists
SPR-534058: New serial number is generated when adding configuration in SolidWorks - regardless if 'update all configurations' is set or not
The SPR should be fixed with 2010 SP05
It says it was implemented on 2011 SP03. Does anyone know when SP03 will be released?