Hello Jeffrey,
We have also had many instances in which our libraries look good but the results did not reflect that. How did the ZMW distribution looked?
In our case many of these samples had contamination issues and many were rescued using a Magbead cleanup. The protocol that we used to rescue the samples can be found on Pacbio's sample net.
http://www.smrtcommunity.com/Share/P...eName=Protocol
Hope this helps