There is a definite bug with the EPDM 2009 SP3.0 add-in in SolidWorks. I do not know the SPR # but as far as I know SolidWorks is aware of the issue. I told all my users to turn off the add-in when not using it. We have only seen the issue while working with large assemblies.
Thank you Lucas.
To test, I will try to upgrade a clone of E-PDM to SP4 next week and I will post here again if the issue is resolved.