Some additional research findings
1. In general the Court does not scan in documents submitted through the ECF but will scan in letters received.
2. The Paper Capture Plugin used does not replace the Creator but does replace the Producer tag with Adobe Acrobat 9.51 Paper Capture Plug-in. A good example is document gov.uscourts.mssd.78493.15.8.pdf where the plugin was used to import http://www.cdc.gov/nchs/data/misc/usvss.pdf which contains an empty creator tag.
3. Paper Capture will insert the document and its bookmarks.
4. PFU ScanSnap Manager 5.1.30 #S1500 was also used to create gov.uscourts.mssd.78493.42.0.pdf but the document was Produced by Adobe PDF Scan Library 3.2